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full protocol - USA National Phenology Network

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1. PRIMARY KEY pkCardID ENGINE InnoDB COMMENT This table stores information about memory cards Table acoustics tblOrganization DROP TABLE IF EXISTS acoustics tblOrganization CREATE TABLE IF NOT EXISTS acoustics tblOrganization kOrganizationID INT NOT NULL AUTO_INCREMENT ldOrganizationName VARCHAR 145 NULL ldAddressLinel VARCHAR 145 NULL ldAddressLine2 VARCHAR 145 NULL ldCity VARCHAR 145 NULL ldState VARCHAR 2 NULL ldZip VARCHAR 5 NULL ldofficePhone VARCHAR 12 NULL ldOfficeEmail VARCHAR 125 NULL 2 Hh h hhh FO OP PRIMARY KEY pkOrganizationID ENGINE InnoDB COMMENT Store the organization name and contact info here Table acoustics tbProject DROP TABLE IF EXISTS acoustics tbProject CRE E TABLE IF NOT EXISTS acoustics tbProject kProjectID INT NOT NULL AUTO_INCREMENT kOrganizationID INT NULL ldProjectName VARCHAR 145 NULL PRIMARY KEY pkProjectID gt CONSTRAINT fk_tbProject_tblOrganizationl FOREIGN KEY fkOrganizationID mh Hho BD REFERENCES acoustics tblOrganization pkOrganizationID ON DELETE NO ACTION ON UPDATE NO ACTION ENGINE InnoDB COMME
2. OK Cancel Apply Help ee b Click on the User DSN tab and click Add This will store the connection information associated with your Windows user log in Then choose MySQL ODBC 5 1 Driver or higher Then click Finish 189 SOP 8 Automated Sound Detection and Classification Appendix S8 A Creating a MySQL database continued Cc ee Select a driver for which you want to set up a data source Name Microsoft Text Driver bt csv Microsoft Text Treiber bt csv Microsoft Visual FoxPro Driver Microsoft Visual FoxPro Treiber MySQL ODBC 5 1 Driver SQL Server SQL Server Native Client 10 0 m Fill in the dialogue box that appears Here you ll enter what name you want to give this connection we called it acoustics the default for the dbUpload Download functions and a short description You will also enter the server name and port see Set up a cloud database above The User name and password are the strings associated with the database itself When you enter the server and port and fill in the correct identity the name of your database should appear in the database box 190 SOP 8 Automated Sound Detection and Classification Appendix S8 A Creating a MySQL database continued MySQL Connector ODBC Data Source Configuration ammm a 6 Connector ODBC acoustics Xeround doud database instance 12345 db xeroul Port 19002 CoopuUnit
3. DY i FOR EIGN KEY fkSurveyID REF gal ON CO CR C EkS M ENCES ETE NO ACTION A NO ACTION nnoDB F E Iau EA TE INDEX r veyID ASC acoustics AUTO_INCR ENUM Original Hi acoustics tblSurvey gt fk_tlbEvents_tblSurveyl_idx tblArchive tblArchive EMENT f ts NULL La Events_tblSurveyl pkSurveyID For archiving sound clips extracted from surveys ON acoustics tblArchive Table acoustics tblPriors DROP TABLE CR F acoustics IF EXISTS ry F TABLE IF NOT EXISTS Lo kSp 1dP cationID INT eciesID INT NOT NUL NOT NULL T Li ld ld ld P D P A rior DECIMAL 5 5 NULL riorDate DATETIME NULL riorDescription VARCHAR riorType ENUM Habitat RY KEY fkLocationID RAINT r r f KEY fkLocationID ES G NO ACTION NO ACTION E EY fkSpeciesID K zal CR fkSpeciesID G NO ACTION NO ACTION nnoDB E acoustics tblPriors 45 acoustics tblLocation ES acoustics tblSpecies tblPriors r NULL
4. Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWd 2 ct Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWauto 8 ct Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWauto 2 ct Save the Binary Point Template list to a local drive with writeBinTemplates Once the templates have been made they can be saved to a local directory with the writeBinTemplates function gt writeBinTemplates templates BiINtemplates dir C Users jkatz3 Dropbox LabDemo WAVclips Templates Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWd1 0BIN bt Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWpoint1 0BIN bt Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWd 8BIN bt Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWauto 5BIN bt 147 SOP 7 Acoustic Template Creation Upload the Correlation Template list to the database The entire correlation or binary point template can be uploaded to the database using the function dbUploadTemplates since it usually consists of relatively few sample points compared to a wav file of equal duration The following example will demonstrate the process on a correlation template but the process is identical for binary point templates Use the args call to see the arguments for the dbUploadTempl
5. iesID ASC CREATE INDEX fk_tb1T emplate fkLocationID ASC CREATE UNIQUE INDEX E _tblSpeci esl_idx ON _tblLocationl_idx ON RENCES acoustics tblSpecies pkSpeciesID ELETE NO ACTION PDATE NO ACTION AINT fk_tblTemplate_tblLocation1 IGN KEY fkLocationID RENCES acoustics tblLocation pkLocationID ELETE NO ACTION PDATE NO ACTION InnoDB Store templates and template metadata acoustics tblTemplate acoustics tblTemplate fldTemplateName_UNIQUE ON acoustics tblTemplate fldTemplateName AS Cy sp E Table acoustics tblRecorder DROP TABLE IF EXISTS acoust CREATE pkRecorderID INT NOT NUL TABLE IF NOT EXISTS SM2 T oz ics tblRecorder acoustic L AUTO_IN s tblRecorder CREMENT COMM ENT This number is assigned automatically and serves as the primary key for the table fldManufacturer VARCHAR 45 NULL COMMENT The manufacturer of the recording unit e g Wildlife Acoustics fldModel VARCHAR 45 NULL COMMENT The model of the recording unit e g ldYearPurchased YEAR NULL COMMENT The year the unit was purchased Fr Fh ldOperationStatus gt ENUM In Service Needs Repair Recycled NULL COMMENT The status of the
6. Another method would be to read in all correlation templates in the directory in which case you need only specify the directory CORtemplates lt readCorTemplates dir C Users jkatz3 Dropbox LabDemo Templates MABI2_A_062510 wav The resulting object is a template list ready to be used for correlation analysis Read binary point templates from the local disk BINtemplates lt readBinTemplates files c BTNWd1 0 BTNWd1 0 ct BTNWpartial BINWpartial ct 165 SOP 8 Automated Sound Detection and Classification BINWd 8 BTNWd 8 ct BTINWd 5 BTNWd 5 ct BTINWd 2 BTNWd 2 ct BTNWauto 8 BINWauto 8 ct BTNWauto 2 BINWauto 2 ct dir C Users jkatz3 Dropbox LabDemo Templates parallel FALSE BINtemplates lt readBinTemplates dir C Users jkatz3 Dropbox LabDemo Templates MABI2_A_062510 wav parallel FALSE Download binary point and correlation templates from the database If your templates are stored in the database download them with the dbDownloadTemplates function There are several approaches to this To download all templates for correlation analysis specify either the file extension ct or bt or the label COR or BIN in the by type argument This function demands that all templates entering a list have the same FFT parameters Download all correlation templates from the database with the appropriate FFT parameters CORtemplates lt dbDownloadTemplates d
7. Date NULL fkSpeciesID T r fk_tblPriors_tblLocation1l C pkLocationID fk_tblPriors_tblSpecies1 pkSpeciesID Store site amp species INDEX LOC ationID ASC r EFA ry INDEX ASC r fk_tblPriors_tblLocationl_idx fk_tblPriors_tblSpecies1l_idx specific priors here ON acoustics s tblPriors ON acoustics tblPriors 198 SOP 8 Automated Sound Detection and Classification Appendix S8 B Database Schema continued Table acoustics tblResult DROP TABLE IF EXISTS acoustics tblResult CREATE TABLE IF NOT EXISTS acoustics tblResult pkResultID INT NOT NULL AUTO_INCREMENT fkSurveyID INT NULL fkTemplateID INT NOT NULL fkPersonID INT NULL COMMENT fldDateTime DATETIME NULL COMMENT From findPeaks corresponding to song event Vig fldTimeZone CHAR 3 NULL fldTimeS SSS FLOAT NULL COMMENT From findPeaks of survey for song event fldScore DECIMAL 5 3 NULL COMMENT from findPeaks or point matching score fldHit TINYINT 1 NULL COMMENT from findPeaks 1 O score lt cutoff fldVerified TINYINT 1 NULL COMMENT user similar function 1 manually verified to be O manually verified to be false positive detection E ENUM COR BIN NU Current choices are cross correlation aryPtMatch
8. Data Analysis and Reporting Revised by Geri Tierney Changes Justification Brian Mitchell Kathy Gerst Geri Tierne Abe Miller Rushing Geri Tierney Added Appendix A Editorial changes Replaced Julian date with day of year Suggested flagging questionable data points Adjusted procedure for multiple peaks Clarified that abundance data will be difficult to extract by automatic detection of audio data Added error term to event dates 248 SOP 12 Data Analysis and Reporting Appendix 12 A Selected Phenophases for NETN Species NETN monitors phenology using phenophases defined by the USA National Phenology Network USA NPN These phenophases vary by species lifeform Specific definitions of each phenophase are found on species information sheets which are available for download from the Nature s Notebook website www nn usanpn org This program is designed to collect extensive phenological data on 27 core species To focus data analysis phenophases shown in bold are selected as the highest priority for data analysis These selected phenophases are expected to respond most noticeably to changing climate and provide sufficient data for analysis Table S12 A 1 Selected phenophases for deciduous trees and shrubs prioritized for data analysis neces Red maple Sugar maple Hobblebush Beach rose Breaking leaf buds x x x x Leaves x x X X Increasing leaf size x x x x Colored leaves x x
9. Local site Remote site gt oo l Status window amp bin gt S bost Remote site server 5 cdrom gt see window Filename Fil Filename Filesize Filetype Last modified Permission Ow 5 bin boot S cdrom Not connected to any server w dev etc Jen 4 files and 23 directories Total size 38 4 MB Not connected Server Local file Directio Remote file Size Priority status Queued files Falled transfers Successful transfers ma Queue empty To create a new connection click on the Site Manager button in the upper left highlighted in red above In the Site Manager click on the New Site button which will be listed under My Sites rename it phenocamFTP This will be saved for future sessions Fill out the menus on the right so that they match the configuration below and press Connect a DAR g Host Username Password Port Quickconnect A Site bisa la Select Entry General Advanced Transfer Settings Charset v 1 MySites phenocamFTP Host phenocam sr unh edu Port Protocol FTP File Transfer Protocol j Encryption Use plain FTP Local site v we Logon Type Anonymous Bin User gt boot cdrom Password gt w dev Account Filename Comments iodified Permission Ow bin New Site New Folder boot New Bookmark Rename cdrom ever 5 dev Delete Copy y etc a J SEE 4 files and 23 din Connect
10. Make sure to create duplicate backups of all recordings for example download the files to a computer hard drive or external hard drive and back the files up to a separate external hard drive 108 SOP 6 Deployment and Maintenance of Autonomous Recording Units as well In addition a copy of the recording schedule file for the Song Meter ARU should be stored with the data collected by that ARU The naming convention for these files is PARKXXXX_YYYYMMDD SET For example ACAD3191_20100527 SET is the settings file that was used at the ACAD site 3191 starting on 27 May 2010 A new version should be saved whenever the deployment settings are changed Deployment settings should never be changed within a monitoring season and should only be changed with careful consideration regarding the compatibility of a new schedule with existing data Depending on the speed of the computer being used download may take a substantial amount of time up to 30 minutes for a 32 GB card Keep this in mind if downloading will be done in the field which might be the case if you do not have enough SD cards to switch all full ones for empty ones in one visit Once the audio data has been downloaded files on the card are erased in order to reuse the cards Occasionally a card will malfunction and fail to record data properly In this case it may help to reformat the card upon download The Olympus unit has a card reformatting function to reformat in the field
11. Safety Manager and he or she will try to find a field partner for you For monitoring at designated accessible sites that are on or near trails monitoring may be done alone or with a partner Daily Communication and Planning Monitoring staff are expected to carry a reliable communication device In most NETN parks a personal cell phone can be used At ACAD cell phones are not reliable and NETN has purchased a Personal Locator Beacon PLB and SPOT GPS Messenger that can be checked out by volunteers The SPOT GPS Messenger can be used for checking in at the end of the field day as well as sending an emergency signal if needed while the PLB is a more reliable emergency signaling device Monitoring staff must fully understand how to operate all communication devices before heading into the field All modes of communication must be fully charged and tested at the beginning of each day APPA also has poor cell phone coverage but it is not logistically possible for NETN to provide emergency communication devices for this park Monitoring staff must notify the park Natural Resource Manager or a designated individual RM DIJ with an expected schedule for field work including sites or routes to be surveyed prior to commencement of site visits Phenology monitoring occurs frequently daily to weekly during the growing season and may be weather dependent so the expected schedule need not specify exact dates For example a seasonal phenology monit
12. click dens ifelse dens Where the allows the user to add FFT parameter arguments These arguments may include e wl to change window length e g wl 1024 must be a power of 2 Common wls are 128 256 512 and 1024 e ovlip to change window overlap e g ovlp 50 must be a percent between 0 and 99 Common ovlps are 0 25 50 and 75 e wn to change window function e g wn hamming others include the default hanning blackman rectangle and triangle Detection of some calls may be improved by changing the FFT window length FFT overlap or FFT window function The default FFT parameters are typically suited for vocalizations that span a frequency band gt kHz and have durations gt 1 second Vocalizations with durations lt 1 second might benefit from increased time resolution which is achieved with smaller window Fast Fourier Transformation 124 SOP 7 Acoustic Template Creation lengths lt 512 Vocalizations that span lt 1kHz may benefit from more frequency resolution which is achieved with longer window lengths gt 512 Increasing the overlap for longer window lengths allows some time resolution to be returned Overlap is specified as a percentage ranging from 0 to 99 typical values are 0 50 75 and 95 Specifying new FFT parameters in the template will pass the parameters to the survey as well Begin by calling the function adding values to arguments where no default
13. in the second box and then add each individual NETN park in the third box All data from shared public and private sites within participating NETN parks should be included If a park or a site seems to be missing from the dataset that park or site may not be properly affiliated with the NPS NETN network and the NETN data manager or park coordinator should contact USA NPN NCO staff to correctly register this affiliation In 2014 or later USA NPN plans to provide processed data variables including estimated start and end dates for phenophase events in addition to the raw time series dataset At that time NETN will evaluate USA NPN estimation methods and decide whether to adopt those methods and use USA NPN processed datasets for analysis and reporting For now NETN will calculate event dates in a simple and straightforward fashion as follows See Appendix A for monitored phenophases As of 2013 USA NPN data contact is Alyssa Rosmartin alyssarosemartin gmail com 243 SOP 12 Data Analysis and Reporting In order to avoid bias due to differences between the solar and Gregorian calendar and precession of the equinoxes event dates are calculated and analyzed as days past winter solstice Henebry et al 2009 For user friendly reporting event dates are converted and shown as day of year for a non leap year in graphs and data summaries To account for unsampled days between sampling visits event dates are estimated to occur ha
14. recorded on day 5 was followed by no recorded on day 8 the end date is day 6 Phenophase duration For each individual plant or animal species monitored at a site estimate phenophase duration as the period in days between the start date and end date for that phenophase For example if the 244 SOP 12 Data Analysis and Reporting start date is day 7 and the end date is day 28 duration is 21 days Phenophases may have multiple start and end dates during a season NETN may choose to consider multiple phenophase start and end dates within a season to be a continuous event for a particular phenophase This may be useful for phenophases which are difficult to detect i e many animal phenophases Phenophase peak For each individual plant or animal species monitored at a site estimate phenophase peak as the date corresponding to the midpoint of the interval for which abundance is reported to be the highest value recorded in the current season Calculate the peak period to include the days in the prior and next intervals divided by two and then rounded down to the last whole number Round the midpoint down to the last whole number For example if Open flowers recorded as gt 95 from day 8 until day 28 was preceded by 75 94 on day 6 and followed by 50 74 on day 29 the peak is estimated to be day 17 If this phenophase never reached gt 95 in a given year peak would be calculated on the highest category reached that year
15. Appendix S8 B Database Schema continued CREATE INDEX fk_tblRecordings_tblLocationl_idx ON acoustics tblCardRecorder fkLocationID ASC CREATE INDEX fk_tblFieldRecordings_tblCardl_idx ON acoustics tblCardRecorder fkCardID ASC CREATE UNIQUE INDEX pkCardRecorder_UNIQUE ON acoustics tblCardRecorder pkCardRecorderID ASC CREATE INDEX fk_tblCardRecorder_tblPrograml_idx ON acoustics tblCardRecorder fkProjectID ASC Table acoustics tblSurvey DROP TABLE IF EXISTS acoustics tblSurvey CREATE TABLE IF NOT EXISTS acoustics tblSurvey pkSurveyID INT NOT NULL AUTO_INCREMENT fkCardRecorderID INT NULL fldSurveyLength FLOAT NULL COMMENT Survey recording duration in seconds fldOriginalDateModified DATETIME NULL COMMENT Date time and time zone of when the original file was created closed and saved This is the end time of the survey fldTimeZone CHAR 43 NULL fldOriginalRecordingName VARCHAR 256 NULL COMMENT If survey file name changed during format conversion or to match name standard record original name here fldSurveyName VARCHAR 256 NULL COMMENT Current survey file name fldRecordingFormat ENUM WAV MP3 WA
16. Change Plan Ask Us Username CoopUnit P Change Password Creation Date 2012 10 18 12 03 29 Size 10 MB Data Center Amazon EC2 US East Virginia Connecting to your DB Instance Thresholds 80 External DNS hostname Data S26 instance db xeround com 19055 60 95 CPU rs __ Internal DNS hostname 80 int instance S db xeround com 19055 Connecti Ss TT Clicking on the hostname would connect you to your instance with Auto Scale Disabled Learn more phpMyAdmin Look for the heading External DNS hostname the link below it provides the server name e g instance12345 db xeround com as well as the port number e g 19002 When you click 186 SOP 8 Automated Sound Detection and Classification Appendix S8 A Creating a MySQL database continued on that link you will be asked to enter another username and password This username and password is the username and password for the database you created If you have multiple databases each can have their own username and password You will want to keep tabs on this information as well phpMyAdmin User username Password Login After you select a username and password you ll be brought to a the following screen phpMyAdmin I cinstance29243 4b xeround com 19055 Databases SQL Status Users i Export i Import Settings 9 Synchronize Replication Variables Charsets v More 2 as amp Recent tables Change password Se
17. E users jkatz3 Desktop SOSPtemplates s13 wav s14 lt readWave E users jkatz3 Desktop SOSPtemplates s14 wav s15 lt readWave E users jkatz3 Desktop SOSPtemplates s15 wav s16 lt readWave E users jkatz3 Desktop SOSPtemplates s16 wav s17 lt readWave E users jkatz3 Desktop SOSPtemplates sl17 wav s18 lt readWave E users jkatz3 Desktop SOSPtemplates s18 wav s19 lt readWave E users jkatz3 Desktop SOSPtemplates s19 wav s20 lt readWave E users jkatz3 Desktop SOSPtemplates s20 wav s21 lt readWave E users jkatz3 Desktop SOSPtemplates s21 wav 22 lt readWave E users jkatz3 Desktop SOSPtemplates s22 wav 23 lt readWave E users jkatz3 Desktop SOSPtemplates s23 wav and make a single file containing all 23 examples of songs survey lt bind noise sl noise s2 noise s3 noise s4 noise s5 noise s6 noise s7 noise s8 noise s9 noise s10 noise sll noise s12 noise s13 noise s14 noise s15 noise s16 noise s17 noise s18 noise s19 noise s20 noise s21 noise s22 noise s23 noise Then run sccCor or binaryPtMatch assigning the output to an object scc lt sccCor survey survey templates templates and then run findPeaks assigning the output to an object pks lt findPeaks score obj scc followed by compareTemplates assigning the output to an object comp lt compareTemplates pks L pks cutoff 0 3 tol 2 0 The argument for peak grouping tolerance t
18. OK Cancel Server Local file Directio Remote file Size Priority Status Queued files Failed transfers Successful transfers Queue empty ee This will now open a connection to the PhenoCam server In the status window you will see some print outs regarding the connection Normally you would see the folders and directory listings for the remote server however Phenocam is setup to be invisible for security purposes Therefore don t be alarmed by the status message Error Failed to retrieve directory listing 238 SOP 11 Data Management and Quality Assurance Quality Control Appendix 11 C Instructions for transferring images to the PhenoCam Server via FTP continued Failedtransfers Successful transfers The URL for the ftp directory for your site will be found in the following subfolder data sitename For the purposes of illustrating a transfer we will just use a test folder called ftptest or data ftptest In the Remote site window enter data ftptest and press Enter This will create a small directory listing underneath 239 SOP 11 Data Management and Quality Assurance Quality Control Appendix 11 C Instructions for transferring images to the PhenoCam Server via FTP continued phenocamFTP phenocam sr unh edu FileZilla Amiel e 4 amp Hera Username Password Retrieving directory listing PWD 257 TYPE z 200 Switching to Binary mode PASV 227
19. images from Harvard forest and other factors we use a moving window approach that assigns the 90 percentile of all daytime gcc values within a three day window to the center day per90 resulting in three day gcc For a long term time series a value every third day is sufficient for characterizing seasonal canopy development and avoids the auto correlation that would occur in a daily dataset of this type Sonnentag et al 2012 stress that the effectiveness of per90 depends largely on data availability thus high frequency image archives are needed ideally one image every 30 min during daylight hours as specified in the Selecting Deploying and Maintaining Automated Digital Cameras SOP Within PCIP select a window of 3 days and check the box for 90 perce within Calculation Options Detecting phenophases Figure 10 2 illustrates a typical gcc time series as derived from a Harvard Forest webcam with the four principal phenophases indicated below Winter baseline values are typically in the range of 0 33 to 0 40 where lower values are expected in a 100 deciduous canopy as compared to this partially coniferous forest Spring green up demonstrates a very rapid increase from the baseline 0 36 to the summer peak 0 46 These gec values gently decline with increasing chlorophyll and aging darkening of the leaves throughout the summer dropping to a value of 0 42 At the beginning of fall leaf coloration rapidly decreases gec val
20. 0 871 0 611 0 633 0 668 0 655 0 599 0 634 0 642 0 581 s15 0 629 sl6 0 594 0 626 0 568 0 612 0 627 0 639 0 557 0 568 0 559 0 628 0 578 0 632 0 589 0 603 0 599 0 999 0 553 0 604 0 550 0 583 0 541 0 556 0 617 sl6 0 608 s17 0 590 0 624 0 479 0 493 0 615 0 557 0 588 0 555 0 461 0 527 0 501 0 646 0 495 0 574 0 623 0 537 0 853 0 621 0 666 0 562 0 552 0 569 0 515 s17 0 574 s18 0 695 0 804 0 620 0 588 0 816 0 646 0 676 0 627 0 632 0 734 0 695 0 801 0 582 0 776 0 668 0 602 0 619 0 921 0 706 0 728 0 718 0 797 0 723 s18 0 703 s19 0 645 0 693 0 506 0 507 0 725 0 577 0 632 0 564 0 547 0 622 0 582 0 685 0 541 0 660 0 655 0 537 0 681 0 720 0 947 0 622 0 648 0 688 0 597 s19 0 634 s20 0 659 0 761 0 640 0 601 0 704 0 655 0 607 0 644 0 704 0 806 0 759 0 698 0 620 0 769 0 591 0 581 0 553 0 730 0 639 0 859 0 640 0 707 0 811 s20 0 684 s21 0 629 0 696 0 544 0 554 0 669 0 592 0 600 0 549 0 545 0 635 0 591 0 672 0 534 0 666 0 631 0 536 0 575 0 697 0 628 0 640 0 905 0 684 0 606 s21 0 625 s22 0 664 0 779 0 568 0 538 0 757 0 595 0 631 0 603 0 590 0 677 0 643 0 732 0 553 0 721 0 632 0 552 0 599 0 823 0 672 0 707 0 659 0 817 0 693 s22 0 661 s23 0 650 0 771 0 643 0 619 0 712 0 685 0 582 0 670 0 712 0 820 0 771 0 708 0 613 0 772 0 579 0 615 0 566 0 751 0 618 0 799
21. Appendix S8 C Downloading and Installing R The latest version of R for Windows is available at http cran r project org bin windows base Make sure that you have administrative rights to your computer and then double click the installer file Run the installation using the default options this will install the 32 bit version if you have a 32 bit operating system and both the 32 and 64 bit versions if you have a 64 bit operating system Once R installs launch the program and select Packages Set CRAN Mirror A window will open select the location nearest to you Select Packages Install Packages In the window that appears select all the packages you might need hold down the Ctrl key to select multiple packages and click OK 1 tuneR 2 plyr 3 RODBC When asked if you d like to use a personal library click Yes and allow R to create the personal library if needed R will download the packages 201 COT tblSurvey tblTemplate combineBinTemplates makeBinTemplate combineCorTemplates makeCorTemplate fileCopyRename tblResult writeBinTempiates readBinTemplates unis readCorTemplates sccCor binaryPtMatch combine CorTemplates findPeaks specScorePlot collapseClips showPeaks Results writeCorTemplates makeCorTemplate combineBinTemplates makeBinTemplate Database interactions in orange Inputs and outputs in blue Template m
22. BOHA Mary Raczko MABI Christina Marts MABI Joan Haley MABI Melissa Fellows MABI Jen Stainton MORR Bob Masson ROVA Dave Hayes SARA Chris Martin WEFA Greg Waters Position NETN Inventory and Monitoring Program Manager SERC ACAD Science Coordinator NETN Science Communication Specialist NETN Data Manager NPS I amp M contact for Paperwork Reduction Act compliance Biologist Chief of Resource Management SERC Program Development Director Volunteer Coordinator Director Schoodic Bird Ecology Lab Environmental Monitoring Coordinator Natural Resource Specialist Resource Management Coordinator Stewardship Program Manager Volunteer Coordinator Resource Manager Forest for Every Classroom Partner Teacher Teacher Biologist Natural Resource Manager Integrated Resource Program Manager Horticulturist Email Brian_Mitchell nps gov Abe_Miller Rushing nps gov Ed_Sharron nps gov Adam_Kozlowski nps gov Margaret_Beer nps gov Bruce_Connery nps gov David_Manski nps gov bill sercinstitute org Jonathan_Gormley nps gov seth sercinstitute org Fred_Dieffenbach nps gov Casey_Reese nps gov jodell appalachiantrail org Marc_Albert nps gov Mary_Raczko nps gov Christina_Marts nps gov Joan_Haley partner nps gov Mfellows wuhsms org jstainton wuhsms org Robert_Masson nps gov Dave_Hayes nps gov Chris_Martin nps gov Greg_Waters nps gov Additional contacts Name Ellen Denny Alyssa Rosmartin Therese Donovan Andrew
23. Click OK to the FTP Folder Error message The anonymous login does not have read permission but it is possible to move files to the location despite the error File Edit View Tools Help Organice FY Favorites BH Desktop E My Documents Ti Download amp Google Drive B Videos 1E Computer amp Local Disk C3 c Local Disk 0 G mitcheltor inpenatG9996 users H G NETN Test Web Site T G NETN Staging Web Site M GP NETN Z Drive N inpnetnserer 2 D ftpten on phenocam sr unh edu h 0 items 10 The ftp site now shows under Computer on the left side of Windows Explorer and it is possible to copy paste or click and drag files to this location Files will be visible after being copied to the ftp site but refreshing or moving navigating away from the site and back will cause the files to not be visible even though they have been moved Note that we have imposed limited permissions on these FTP folders so directory listings using ls and pwd will not work Using an FTP client You can also do a manual FTP file transfer using a number of different software programs We will use the free FileZilla software which you can download at http filezilla project org Here is a screen shot of the program interface 237 SOP 11 Data Management and Quality Assurance Quality Control Appendix S11 C Instructions for transferring images to the PhenoCam Server via FTP continued FileZilla k
24. Multiple peaks in a given year complicate this measure in this case calculate each peak separately However if abundance fluctuates only between the highest and second highest categories reached that year NETN may ignore these minor dips and calculate peak using the earliest and latest dates in which the highest abundance category is reached Audio data Audio recordings are processed using an automatic detection procedure as described in SOP 8 Automated Sound Detection and Classification The resulting dataset contains a time series of phenophase detections This audio dataset is essentially continuous so no adjustment is needed for intervals between sampling dates For each animal species of interest at an ARU site relevant phenophase start and end dates are estimated to be the first and last dates on which the phenophase was detected and phenophase duration is calculated as the period between start and end dates It is difficult to estimate abundance from audio recordings using automatic detection NETN may estimate an index of abundance based on calling frequency However overlapping calls are problematic and will increase error rates due to false negatives but perhaps false positives also Camera data Manual analysis of images from automated cameras aimed at individual plants is recorded and submitted to the National Phenology Database This dataset resembles observer data and event dates are calculated as described above for obser
25. Symptoms may include a bull s eye rash around the tick bite doesn t always occur tingling or numbness in extremities a spotted rash on extremities bad headaches high fever joint aches stiff neck fatigue or swollen glands If you develop a combination of these symptoms soon after a tick bite seek medical attention 42 SOP 1 Safety adult adult female male nymph Lone Star Tick Amblyomma americanum Kx Dog Tick Dermacentor variabilis Re Figure S1 1 Tick species found in the eastern US Considerations for using repellents containing DEET e DEET products have been widely used for many years these products have occasionally been associated with some adverse reactions Frequently reported reactions are about skin or eye irritation There have been reports of central nervous system problems e By using products with lower concentrations of DEET and by applying as little of the product as needed for your outdoor work you can reduce your expose to DEET e Products with about 20 30 DEET are considered effective for most insects but do not seem to be effective against the black legged or deer tick Ixodes scapularis e Generally products with about 20 30 DEET are considered safe for adults except for those with allergies to DEET products when applied as directed 43 SOP 1 Safety Considerations for using repellents containing permethrin e Products containing permethrin are for use on c
26. This timer should be visible on the display screen If it lists less time such as 34 hours stop the recording and double check that the file destination is set to the microSD card and then reset all of the timers However if you are using a 2 GB SD card or microSD card then it will have the same amount of memory as the internal memory and there will be no difference in the countdown time The last possibility an SD card smaller than 2 GB would mean that the countdown timer should indicate less than 34 hours The timer may also list a different time remaining if a different file format or quality is selected when setting up the recordings For help setting the Olympus Unit to record on a schedule other than 24 hours a day consult the Olympus Digital Recorder User s Manual provided by the manufacturer 99 SOP 6 Deployment and Maintenance of Autonomous Recording Units Deployment of Song Meter SM1 or SM2 ARU 1 Microphone 2 Display screen for programming 3 Weatherproof case 4 Wire leading to external battery Schedule Button Set Button Exit Button Select Up Down Button Display Screen oy ee E necercrecevectresy _ osXL LS 5 Vg e 6 Wake Button 7 SD Slot A and B Figure S6 5 The Song Meter SM1 Unit The currently available SM2 is similar see user manual for button layout and microphone ports Before you go into the field Set Date and Time Manually set the time and date accor
27. latitude of the location latitude and longitude u The longitude of the location ULL COM tional 6 Eag The to get 1 T HAR Datum EN T socationT locati PRI ENGINE COMMEN on ARY KEY InnoDB T UM WGS84 NAD27 The datum of the latitude and longi ENUM Site Template for a monitoring site location of a recording made expressly for creating a template ype Site pkLocationID gt This table stores information about about all comment truncated to get latitude and longitude i NAD83 GRS80 NULL DEFAULT de Default is WGS84 LL COMMENT Template r tu NU for L locations i key for this table name or description of the Tab le acoustics tblSpecies 192 ar F The 6 digit Google Google WGS84 1 r The type of the the nt SOP 8 Automated Sound Detection and Classification Appendix S8 B Database Schema continued DROP TABLE IF EXISTS acoustics tblSpecies CREATE TABLE IF NOT EXISTS acoustics tblSpecies pkSpeciesID INT NOT NULL AUTO_INCREMENT COMMENT The unique number assigned to a specific species This number is automatically assigned and serves as the primary key for this tab
28. ldLikelihood DECIMAL 4 4 g detected wit bi bei fFldAnalysisType gt n n detected with this score a prior b h this score added from showPeaks true positive detection Time of day Time since beginning score gt cutoff or iL COMMENT NULL COM sccCor ENT Looked Ta Type of analysis or binary template matching Probability of t not verified distribution up in empirical ldPosterior DECIMAL 4 4 NULL COMMENT Likelihood of the species being Potential priors include occupancy probability phenological encounter probability fldCutoffValue DECIMAL 5 3 NULL PRIMARY KEY gt pkResultID CONSTRAINT fk_tblSpeciesResults_tblTemplates1 FOREIGN KEY fkTemplateID REFERENCES acoustics tblTemplate pkTemplateID ON DE E NO ACTION ON UPDATE NO ACTION CONSTRAINT fk_tblResults_tblSurveyl FOREIGN KEY fkSurveyID REFERENCES acoustics tblSurvey pkSurveyID ON DELETE NO ACTION ON UPDATE NO ACTION CONSTRAINT fk_tblResults_tblPersonl FOREIGN KEY fkPersonID REFERENCES acoustics tblPerson pkPersonID ON DELETE NO ACTION ON UPDATE NO ACTION ENGI
29. network location or FTP ste 5 Click Next Specify the location of your website Type the address of the website FTP site or network location that this shortcut will open Internet or network address View examples 6 Enter the ftp address in the Internet or network address text box e g ftp phenocam sr unh edu data ftptest and click Next 235 SOP 11 Data Management and Quality Assurance Quality Control Appendix S11 C Instructions for transferring images to the PhenoCam Server via FTP continued i E Specify a User Name and Password if Required Most FTP servers allow users to log on anonymously with limited access to the server Do you want to log on anonymously F Log on anonymously User name Anonymous 7 Click Next What do you want to name this location Create a name for this shortcut that will help you easily identify this network location ftp phenocam sr unh edu data ftptest Type a name for this network location 8 Rename the location if desired and click Next 236 SOP 11 Data Management and Quality Assurance Quality Control Appendix S11 C Instructions for transferring images to the PhenoCam Server via FTP continued fie fda View Tools Help An error occurred opening that folder on the FTP Server Make sure you have permeswon to access thet folder ASCE mode 9
30. public in natural history observation while providing a cost efficient source of monitoring labor Phenology is well suited to monitoring by citizen volunteers because many phenophases are easy for the public to observe with minimal training Data from automated sensors complement data collected by volunteers by providing data for quality assurance quality control and by facilitating monitoring at difficult to access sites We monitor phenological status and intensity or abundance using phenophases defined by USA NPN Appendix A rather than the more traditionally observed phenological events Historically phenology has often been recorded as the timing of specific phenological events that is precisely defined points in the annual life cycles of plants or animals such as first and last flower or first arrival and departure of migratory animals e g Sparks and Carey 1995 The utility of this approach is limited by several factors including the lack of correspondence between a first or last event and the overall phenological behavior of individuals or populations Moussus et al 2010 The observed timing of phenological events can be affected by many factors including population size the size of individuals sampling effort and outlier effects Tryjanowski et al 2005 Miller Rushing et al 2008a van Strien et al 2008 Blumstein 2009 These confounding factors can make it difficult to quantify the relationship between phenology and cl
31. record as Full sun Mostly sun Half shade Mostly shade or Full shade For trees record as Open grown tree grows under open sky unshaded by other trees Forest canopy tree grows next to other trees of similar height forming a continuous canopy or Forest understory tree grows in shade below taller trees Wild Does this individual plant appear to be a wild plant growing from a seed brought in naturally by wind water birds or animals Most horticultural plants in gardens and parks are intentionally planted by humans and therefore not wild although often so called weeds were brought in by natural forces and can be considered wild Watered Does this individual plant get supplemental water Ideally plants monitored by NETN will not be given supplemental water Record for unknown Y for yes or N for no Fertilized Does this individual plant get supplemental fertilizer This is likely to apply only to plants in a park or garden Ideally plants monitored by NETN will not be fertilized Record for unknown Y for yes or N for no Gender If this plant species is dioecious has male and female flowers on separate plants indicate whether this individual has only male flowers only female flowers or both types Of the species targeted for NETN monitoring rockweed is dioecious and red maple and sugar maple may be dioecious All other NETN species have both male and female flowers on the same pla
32. their park s experience and any problems encountered Prior to the meeting either NETN or park staff will survey volunteer monitors to assess volunteer satisfaction and solicit suggestions for improving the program including training and data collection NETN is using USA NPN protocols for monitoring phenology by observers NETN staff and cooperators will contact USA NPN NCO staff annually in the late fall or early winter to discuss any changes for the upcoming year NETN staff or cooperators will update the protocol annually to reflect changes It is also advisable to teleconference or meet annually or every other year with other organizations monitoring phenology in the northeastern US such as the Northeast Regional Phenology Network the Appalachian Mountain Club and the New York Botanical Gardens Regular communication with these organizations will facilitate collaboration toward regional phenology goals and protocol and data sharing Any protocol changes must be completed prior to the annual spring training sessions held at participating parks Revision History Version numbers will be incremented by a whole number e g Version 1 30 to 2 00 when a change is made that significantly affects requirements or procedures Version numbers will be incremented by decimals e g Version 1 06 to Version 1 07 when there are minor modifications that do not affect requirements or procedures included in the protocol Add rows as needed for each
33. 192 kbps 90h 180h 360 h 128 kbps 136 h 272 h 544 h WMA Format Recording Mode 8GB micro SD 16GB micro SD 32GB micro SD Card Card Card ST XQ 132 h 264 h 528 h ST HQ 266 h 532 h 1064 h ST SP 532 h 1068 h 2136 h HQ 532 h 1068 h 2136 h SP 1048 h 2096 h 4192 h LP 2084 h 4168 h 8336 h Song Meter Unit Specifications Physical Specifications e Dimensions 8 0 X 8 0 X 2 5 e Weight 2 0 pounds without batteries e Enclosure NEMA Type 1 4 4X and 6 weatherproof vented A self regenerating humidity control device such as Zorb It is required to prevent condensation in some conditions 112 SOP 6 Deployment and Maintenance of Autonomous Recording Units Appendix S6 B Unit Specifications continued e Operating Temp 4 F to 185 F 20 C to 85 C Inside the enclosure avoid exposure to direct sunlight in hot environments Also note that operating range of the batteries used may be narrower Audio Specifications e Channels 2 e Interface 3 pin waterproof connector ground signal 3 3V supply e Bias power 2 5V 2 2K ohm jumper enabled per channel e High pass filter 2 pole butterworth jumper selectable per channel at 2 180 or 1 000Hz e Pre amplifier 2 stage jumper selectable per channel at 0 12 24 36 48 or 60dB gain For sample rates lt 48kHz third stage digitally configurable 0 12dB in 1 5dB steps e Noise 115dBV equivalent input noise e ADC 1V rms full scale 16 bit 90dB SNR e
34. 3 in diameter leaving as many open wire tails as possible at the edge Place it at the bottom of the cylinder and bend the wire tails to hold it in place Make sure that no wires protrude outside of the cage so that the windscreen cloth can be slipped over it without snagging Cut a rectangle of faux fur 10 5 x 6 5 With the faux fur on the inside fold the fabric in half so that the two 6 5 ends are together Use the sewing machine to make a rectangular pouch by sewing along one 6 5 edge and one 5 25 edge Z i leaving the other 5 25 edge open Turn Dy SN the pouch right side out and slip it over ts the wire cage D Cut a second rectangle of hardware cloth Px 9 x 2 5 this will be the windscreen shell holder Again leave the tails attached to one of each length edge and trim the other edges so they are flat Bend the rectangle into a cylinder 3 in diameter this time bend it so that the resulting circular wires are inside the straight wires Use the needle nosed pliers to bend the top row of wire on the finished edge inwards so that the larger cylinder can slip over it Bend every other wire tail on the unfinished edge 90 degrees toward the center of the shape leaving every other wire tail straight 86 SOP 5 Building an Autonomous Recording Unit Prepare the microphone NOTE If using the PA3 or PA3 IL microphone each microphone comes with a 6 foot cable and R
35. 3 ability to load results from R directly into the database system A relational database consists of a set of tables that relate or link to each other Each table contains information about one thing For instance a table called tblPerson stores information about people involved in the acoustic monitoring program These may include people who deploy and operate recording devices people who run analyses etc A table called tblLocation can store information about the locations in which acoustic recordings were made including latitude and longitude the location name and whether the location is the location of a monitoring site or whether the location is a place where a template has been recorded There are several relational database programs on the market Acoustic monitoring programs can rapidly acquire massive amounts of data so space is a key factor in choosing a system This document will describe the database system called MySQL http www mysql com which can be run from a server allowing multiple people to use the same database or from your own computer assuming you have a very large hard drive for storing information If you run MySQL on a server you likely do not need to install MySQL on your hard drive However if you plan to have use a local MySQL database that is one that resides on your local disk you will need to download a copy of MySQL at http www apachefriends org en xampp html along with several other tools This
36. Entering Passive Mode 132 177 243 160 233 67 LUST Local site Remote site data ftptest w 5 5 bin s data 3 ftptest Filename B bin boot Filename Filesize Filetype Last modified Permission Owner Gro cdrom S dev 5 etc amp home 5 lib w lib32 9 libs amp lost found Directory listing failed 4 files and 23 directories Total size 38 4 MB Empty directory Server Local file Directio Remote file Size Priority Status Queued files Failed transfers Successfultransfers 4 wm Queue empty In the local site windows on the left navigate to your own directory containing the photos to be uploaded Select as many or all photos as are needed and then right click to select the Upload option am sr unh edu FileZilla Username Status Retrieving directory listing Response 200 Switching to Binary mode Command PASV Response 227 Entering Passive Mode 132 177 243 160 233 67 Command LIST Local site media pheno archive harvard 2012 08 Remote site data ftptest 807 Be 408 Y B data ftptest Filename L Filename Filesize Filetype Last modified Permission Owner Gro Directory listing failed harvard_2012_08_01_100138 jpg _harwacd 2012 08 N1 103138ino Selected 12 files Total size 3 5 MB Empty directory Server Local file Directio Remote file Size Priority Status Queued files Failed transfers Successfultransfe
37. Ideally it would be a superb example with high signal noise and no interference but if the only example you can find is low quality you can still use it to help you find additional better examples as you acquire more recordings An easy way to find a first template is to order one from the Macaulay Library macaulaylibrary org Alternatively you can use one of your recordings Let s assume you have 122 SOP 7 Acoustic Template Creation a long wav file called MABIO2 A 052710 wav on your C drive and you d like to clip a song of a Black Throated Green Warbler from it Find a candidate song example The R package monitoR has an easy tool for interacting with long several minutes to several hour durations audio files To find one from your own recordings load packages monitoR and tuneR from the package library and call the viewSpec function viewSpec MABIO0O2_A_052710 wav the R gui will display the available menu options Options include moving page by page saving the page as wav files playing the survey and zooming in out Change recording sample rate of the template For both sccCor and binaryPtMatch the sampling rate of the template must match the survey There are a number of ways to confirm that this is the case First if you export a template from the survey the sampling rates will match by default If you order one from the Macaulay library or get it anywhere beside for your survey you can read it into R using t
38. Keep your head and eyes pointed somewhat downward so your head hits obstacles before your eyes Wear pants and long sleeved shirts to protect bare skin Look before you grab vegetation to avoid grasping thorny stems Do not follow closely behind other people to avoid having branches snap back and hit you Crossing streams Injuries from falling and or drowning Do not cross streams that are flowing quickly and higher than mid calf find another route Thoroughly investigate area to find safest crossings Wear appropriate foot gear for stream crossings It is safer to wade through water rather than rock hop across a stream trying to keep your boots dry Unbuckle your pack and be prepared to jettison gear should you lose your balance or fall in Use a sturdy pole or walking stick for balance Working in heat Heat exhaustion sunburn Evaluate the weather forecast each morning and humidity or cold dehydration hypothermia plan field work accordingly Carry and drink plenty of water Take extra breaks during extreme weather events Adjust the work routine to minimize exposure to extreme heat and humidity Take adequate garments for all possible weather conditions Choose clothing that will keep you warm even if it gets wet 58 SOP 1 Safety Appendix S1 B Job Safety Analysis continued Potential Hazards Recommended Action or Procedure Hazard trees Being struck by falling trees or Look up Be alert for wi
39. MABT0O2 MABT03 MABIO04 crlocs Song Meter files Song Meter units record in wac format For these files use the fileCopyRename function to copy the files from the SD card to a holding folder from which you can then convert them to wav The function fileCopyRename has 11 arguments which you can view using the args function gt args fileCopyRename function from to csv dir to csv name NA loc prefix ext CardRecorderID NA kaleidoscope TRUE split channels FALSE metadata only FALSE parallel FALSE lt Soon you will need to convert the wac files to wav files using Wildlife Acoustic s Kaleidoscope software if you will be splitting the channels e g if you have an ultrasonic mic in the right channel and a standard mic in the right channel you should set the split channel TRUE The command should be surveydata lt fileCopyRename from C Users jkatz3 Dropbox UVMacoustics Analysis Recordings to C Users jkatz3 Desktop TestFolder csv dir C Users jkatz3 Desktop MetadataFolder loc prefix MABI02 ext wac CardRecorderID 1 split channels TRUE Sai You can leave the kaleidoscope metadata only and parallel options with their default values for now During the copy process all files will be renamed the specified six digit location prefix followed by the original file s date modified including the time zone The new file names will be PARK HH YY
40. Plants growing in the sun will provide more consistent illumination and image quality The camera field of view may be set to contain the entire plant for a small plant or a section of the plant i e a specific branch of a tree and should be consistent with the field of view from prior years Consider future plant growth and allow space for growth within the field of view To capture flowering phenology consider the geometry of this species flowering parts during camera placement ie nodding flowers may best be photographed from below while upright flowers from above The ideal setback distance from camera to plant will vary with plant size and site layout Table S9 1 provides examples of geometric relationships between camera setback distance camera FOV and image resolution to assist in camera placement If possible the camera should point north to minimize maximize illumination by the sun and minimize lens flare Table 9 1 Example of geometric relationships between camera field of view FOV image size area covered and pixel resolution at two camera setback distances for StarDot NetCam IR camera and Wingscapes PlantCam and TimelapseCam Camera setback Camera setback FOV Image 2 m Wingscapes 5 m Wingscapes Camera Format degrees width 25 m StarDot 100 m StarDot g pixels Total FOV Pixel size Total FOV Pixel size m cm m cm Wingscapes 7 PlantCam Medium 52 2048 1 6 0 1 4 0 2 Wingscapes TimelapseC
41. Routine and emergency communication procedures are explained in the relevant SOPs and monitoring staff are provided with contact information specific to their assigned park The procedures include coordination with park natural resource managers and other designated park staff It also includes a daily check out check in procedure for monitoring staff visiting remote or hard to access locations to ensure that a responsible party knows if someone has not returned from the field activity in a timely manner Due to this advance planning written documentation and training procedures a low score 3 was assigned 52 SOP 1 Safety Appendix S1 A Green Amber Red Risk Assessment continued Contingency Resources Contingency resources include communication equipment and procedures that explicitly involve park rangers park dispatch and 9 1 1 Monitoring staff are required to carry a cell phone but coverage is not complete in many parks At one park with poor cell coverage ACAD monitoring staff can check out a Personal Locator Beacon and SPOT GPS Messenger to facilitate check ins and emergency response At the other park with poor cell coverage APPA logistics prevent providing similar equipment In the worst case scenario an incident involving a solo individual in an area with no cell phone coverage could result in a long delay before emergency services are alerted However monitors use marked sites and routes that are generally on or near
42. SONGMETR SET FILE then press select again Confirm that your schedule has been loaded by pressing schedule and checking the values on the screen and confirm that the presets have been loaded by pressing Set and checking the sample rate and compression settings Change the prefix for each unit to 8 digit code corresponding to the four letter NPS acronym corresponding to this park followed by the four digit USA NPN code corresponding to this site i e ACAD3191 for site 3191 at ACAD press select until the prefix has been set and put the unit to sleep by pressing the wake exit button once Do not leave the monitoring site without completely filling out a Deployment Datasheet including the checklist Maintenance for Olympus and Song Meter ARUs Both Olympus and Song Meter units are visited for maintenance and renewal of batteries and SD cards periodically A full complement of 4 D cell batteries will power the Olympus ARU for approximately 318 hours 13 days of continuous recording in the recommended format 128 kbps MP3 using a 32 GB micro SD card Alternatively a 16 GB micro SD card will be filled after 272 hours 11 days The Olympus units are visited every 7 13 days depending upon observer schedule and size of micro SD card installed Wildlife Acoustics SM units are visited weekly to monthly based on the sampling schedule SD card and battery used An SM1 recording in stereo at a 24 kHz sample rate with compression on i e W
43. a long recording survey for one or more templates of either the same or different species The template search process is sequential so searching for the second template will begin only after the first one finishes The score cutoff can be adjusted at this time if necessary The advantages of searching for multiple templates at once are transfer of coding time to the front allowing for unattended computing the option to directly compare multiple templates or template settings and the option to use the compareTemplates function to rationally choose an optimal template Spectrogram cross correlation will be used for detection of most species however binary point matching may be useful in some cases Due to limitations with R s system interface capabilities sccCor and binaryPtMatch can only take advantage of parallel processing on non Windows operating systems only set parallel TRUE on Linux or MacOS Windows users can run multiple instances of R to achieve a similar effect with each instance scanning a different survey Run only as many instances as CPU cores available Spectrogram Cross Correlation First load the templates into the R workspace The function to do this varies depending on where your templates are stored The function sccCor performs the spectrogram cross correlation It uses the FFT parameters specified by the template If using Linux or MacOS you can set parallel TRUE for faster processing Speed should increase approx
44. access to these minimal requirements on their own Participating parks can opt to make datasheets or binoculars available to volunteer monitors if they wish Monitoring via automated sensors requires additional equipment plant cams webcams and or audio recorders and infrastructure as described in the SOPs Startup Costs and Budget Issues Startup costs are minimal due to the use of volunteer monitors and the data infrastructure of the USA NPN However startup funds are needed for automated recording devices about 100 per plant cam 500 1 000 per webcam 250 for parts to build an Olympus audio recorder unit and 1 250 for a Song Meter audio recorder Legal Requirements Collection of data from the public by federal agencies or their partner organizations is regulated by the Paperwork Reduction Act PRA of 1995 The PRA establishes information policies for data collection and is intended to reduce the amount of paperwork that agencies can request the public to submit The PRA applies to surveys of the general public and does not apply to other data collection by agency staff or volunteers For the purposes of the PRA a volunteer is someone who would be covered by Worker s Compensation if they are in an accident while assisting the agency so NPS VIP s are volunteers while other park visitors are not The trained volunteers participating in this protocol are covered by Worker s Compensation and thus are excluded from the PR
45. adult snakes Should you receive a snake bite from a potentially poisonous snake follow the procedure below e Treat all bites as if envenomation has occurred e Time is of the essence e If working in a team assign one person to use a cell phone to call for assistance Identify the call as a snakebite incident and identify the victim s location and the closest possible point of access for responders e Quickly remove rings watches shoes etc before swelling begins e Immobilize the bitten limb firmly with a splinted elastic Ace bandage and get the victim out of the woods and to a hospital as quickly as possible e Do not use thin circulation restrictive cords pack with ice for long periods more than five minutes or attempt to cut open or otherwise enlarge the fang punctures e Reassure the victim that they will be OK and otherwise attempt to maintain the calm both for the victim and for all others involved e Inacrew situation begin leading the victim slowly out of the woods as soon as the bitten limb has been immobilized Move as slow as necessary to maintain a normal heart rate for the victim Waiting for assistance will only prolong the process of getting proper medical treatment 45 SOP 1 Safety e Ina solitary situation establish radio or telephone contact and relay the necessary information as you walk slowly out of the woods Focus on remaining calm and maintaining a normal heart rate e Itis better to spend you
46. an ID number and information about the template and the template file itself is stored in tblTemplate including 1 Species the species that was recorded Person the person who recorded the template Location the location in which the template was recorded Template name each template must have a unique name Recording date the date in which the template was recorded Recording equipment the equipment used to record the template Original file name the song clip the template was made from Sample rate the sampling rate the song clip was recorded at FFT window length the window length 10 FFT window name the window function applied to each window 11 Template data this is the actual template itself 12 Template type either binary BIN or correlation COR 20 POS OV A Ret The work flow for template creation is as follows e Locate a song that will be used to create template use monitoR to seek a song example to clip e Clip the relevant portion of the recording and save the clip in the Template directory Save as mp3 or wav format e Use the makeBinTemplate or makeCorTemplate functions to build the template e Use the makeBinTemplateL or makeCorTemplateL functions to add a score cutoff and create a template list e Upload the template list to tb Template of the database or save it to the Template directory The first step in choosing a song template is to find an example of a target song
47. any issues before proceeding Days Until Memory full at 24kHz Stereo Compression On WACO 128GB 64GB 32GB 16GB a 182 x 168 4 y 154 140 126 dias 98 84 4 70 ty 56 4 42 4 28 4 ial Days between memory swaps Minutes recorded per hour Days Until Battery Empty at 24kHz Stereo Compression On WACO SM2 Deep Cycle SM2 D cells SM1 Deep cycle SM1 D cells b 182 168 H 154 T 140 126 i f 3 Z 112 N 2 N 8 98 S 3 s4 1 amp 70 2 S 56 a 42 28 14 _ 0 L 0 5 10 15 20 25 30 35 40 45 50 55 60 Minutes recorded per hour Figure S6 6 Days of SM recording time between maintenance visits for standard 24 kHz monitoring based on size of SD card a and battery type b Set Up Recording Schedule To create a recording schedule download the Song Meter Configuration Utility from the Wildlife Acoustics website http www wildlifeacoustics com downloads php and follow the 103 SOP 6 Deployment and Maintenance of Autonomous Recording Units instructions in the user s manual Depending on the taxon and purpose of recording you may find the SM2 option for solar tracking valuable To monitor bats use the SM2BAT ultrasonic package from Wildlife Acoustics which will enable recording rates of up to 192 kHz Such a high sample rate will require more memory than typicall
48. are stored in monthly folders 1 e 01 for January within annual folders i e 2012 within site folders i e ACAD3191 for a camera located at ACAD site 3191 All computer data files are stored in duplicate to guard against data loss from hard drive failure For most data this is accomplished by storing identical mirrored copies on two separate external hard drives For raw image files this is accomplished by storing one copy on an external hard drive and a second copy on the PhenoCam server Hard drives are checked annually prior to the beginning of the field season to insure that both copies are functional Software designed to conduct hard drive health tests can make testing more reliable e g http hddscan com If a drive or a drive sector is found to be bad or failing a new drive is purchased and contents from the remaining good drive copied to it immediately to maintain two functional copies of the data at all times If the PhenoCam server discontinues operation at some future time NETN will store duplicate mirror copies of image files to compensate File naming Maintaining accurate standardized and informative file names plays a pivotal role in managing the large number of digital files generated by the implementation of this protocol To insure files are named consistently the following naming conventions should be rigorously followed Image files Since plantcam field cameras cannot be programmed to assign custom
49. at a designated site by volunteers Markers are replaced periodically as they weather and become damaged or unreadable A general marking procedure is included here but each park decides what specific marking is acceptable The center and corners of a site or a specific route for animal observation may be marked with stakes in the ground or flagging tape on tree or shrub trunks or branches The markers must display a unique label or name for the site location or route written using permanent ink Individual animals are not marked in this monitoring program Individual trees and shrubs may be marked by attaching flagging tape or a small inconspicuous tag to the trunk or a branch Forbs may be marked with a labeled stick or skewers placed in the ground next to the plant Each plant marker must display a unique label or name for the plant written using permanent ink For example the flagging on a tree could be labeled Red maple 1 or Big red Marking must not change the growing conditions of the plant For example avoid placing a broad stake in a location where it could shade or cause root damage to a small plant To set up a patch mark the four corners of a square within the area the species takes up over the ground USA NPN recommends a square that is 3 feet or 1 meter on each side but the square can be smaller Register Site Online at Nature s Notebook After a site is selected park staff register the site online at Nat
50. c cjacca ceasesschsediss aveenaaescd oes a a E aa ao eae Ree a 22 Literat re Cited i ey a hace aa aa a a ls a ete eee Eta 25 IG VISION History oes orcsch Santa octal at iat cea ean anit ort anes a had tei abe 20 dca Sane ch ee 29 Appendix A Monitored Phenophases for NETN Species c ccccccecsseceseceeeeeeseeeeeeeseceseeeeeeenaees 30 Appendix B NETN Phenology Program Contact List ceceecesesseeseesseceseceeeeseeeeeeeeeeseenaeeneeess 35 SOPIT Saleen taa a e aa a a a a a 37 SOP 2 Site Selection and Sep piee 4 non acetyl aracteevaceontunataecccere uty iauadl woosteietcnaesataeenei ats ac ceeatenens 65 SOP 3 Observer Recruitment and Training cccsscssscssssccssesescssacsensccssncesscesacessasseenesees 73 SOP 4 Observation ei uona i i a a a aaa a aana 77 SOP 5 Building an Autonomous Recording UMit eee ceccesceeeeeeeeeeeeceseeeeeeeeeeeeseeesseeneenees 80 SOP 6 Deployment and Maintenance of Autonomous Recording Units ee eeeeeeseereeeeees 93 iv Contents continued Page SOP 7 Acoustie Template Creat om ccytcsens hanhivsipcarencadteliesa a oaluciaeieadeata args a a 119 SOP 8 Automated Sound Detection and Classification 00 0 0 cceeseecceseeeteeeeeeeeeeeeeeceseenseeneeees 157 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras eeeeeee 205 SOP 10 Processing Image Data c isc Seder caesiesvestisetecdh vcessiledchsscaaves vlads nels Ars cece hashcaayeicataaerss 21
51. collection These suggestions are carefully considered and useful suggestions are incorporated into the program In addition sharing program results with observers aids in maintaining enthusiasm and retaining volunteers NETN prepares periodic Resource Briefs describing the status of this Phenology Monitoring Program Briefs are available online at the NETN website http science nature nps gov im units netn education outreach cfm and may be distributed to volunteers In addition the USA NPN website interface includes functions to allow volunteers to visualize and download data submitted by their network of observers and others across the country as well as access USA NPN reports 74 SOP 3 Observer Recruitment and Training Revision History Version Date Revised by Changes Justification 1 00 July 2010 Geri Tierney 1 01 Sept 2010 Geri Tierney Editorial changes 1 02 April 2011 Brian Mitchell Clarified that training for volunteers assisting Geri Tierney with automated recording is not described in this SOP and that volunteers may mark plants but not sites Editorial changes 1 10 Dec 2011 Geri Tierney Removed references to participation by untrained observers Added additional USA NPN training materials 1 11 Jan 2013 Ellen Denny Editorial changes Geri Tierney 75 SOP 4 Observation Northeast Temperate Network Version 1 23 Overview Monitors observe the phenology of plants and animals at d
52. configuration pages Specific instructions for focusing the Stardot NetCam SC can be found in PhenoCam Installation Instructions by Cory Teshera Sterne et al updated April 2012 Frequency of images Canopy images are recorded at least every 30 minutes from 04 00 20 00 hours i e 4 am to 8 pm This frequency is designed to optimize the dataset for canopy analysis using PhenoCam methods which use a 3 day moving window Sonnentag et al 2012 Since day length varies Terminology for these settings varies among camera brands TimelapseCam has manual focus PlantCam does not 210 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras over the course of the season some images before and after the summer solstice will be taken at night These dark images are very small in terms of storage space and are easily filtered out of the dataset prior to analysis Plant cams or other digital cameras aimed at individual plants record images hourly from 8 am to 5 pm for a total of 10 images per day For plant cams in the Setup Menu set Time Lapse Interval to be 1 HOUR and make sure Photo or Video option is set to Photo Image file format size and filename There is always a trade off between resolution and file storage because higher resolution images use more storage space Current recommended file resolution is 1 megapixel For example a digital image that is 1024 x 768 is approximately 1 MP For Wing
53. days GDD regress event date on average temperature for the 30 day period prior to the event in degrees C or cumulative GDD from winter solstice to date of event For plant phenophases include individual plant within site as random effect for animal phenophases include site as a random effect If sufficient data from widely spaced parks exist include latitude as a fixed effect omitting site if necessary To calculate GDD for each day from winter solstice to the event calculate GDD as the average of the daily maximum and minimum temperatures minus the base temperature 10 C For example a day with a high of 22 C and a low of 11 C would contribute 6 5 GDDs Sum these daily contributions to calculate cumulative GDD for the event date Reporting Phenology data are summarized and graphically illustrated in the network s annual Weather and Climate reports After 10 years of data collection results of trend analysis will be included in this report Literature Cited Henebry G M A D Richardson D D Breshears J Abatzoglou J I Fisher et al 2009 Phenological trend estimation a reply to Sagarin Frontiers in Ecology and the Environment 7 296 Schaber J F Badeck D Doktor and W von Bloh 2010 Combining messy phenological time series Chapter 7 in I L Hudson M R Keatley eds Phenological Research Springer New York Pilot data collection began in 2009 247 Revision History Version Date SOP 12
54. e shut the power off and then turn power back on It is also useful to check the status lights for the camera and LAN router sockets Specific instructions for maintaining and trouble shooting the Stardot NetCam SC are included in PhenoCam Installation Instructions by Cory Teshera Sterne et al updated April 2012 Calculated by multiplying by image width in pixels by image length in pixels 211 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras Literature Cited Sonnentag O K Hufkens C Teshera Sterne et al 2012 Digital repeat photography for phenological research in forest ecosystems Agricultural and Forest Meteorology 152 159 177 Teshera Sterne C et al 2012 PhenoCam Installation Instructions https dl dropbox com u 29219356 PhenoCam_Install_Instructions doc Revision History Added metadata collection sheet Revised reference panel procedure now uses simple grey panel Check with Andrew Richardson in 2014 re ongoing research on reference panels Version Date Revised by Changes Justification 1 00 May 2012 Geri Tierney Adapted from Digital repeat photography for phenological research camera deployment and image processing protocol Sonnetag and Richardson June 2011 PhenoCam Installation Instructions Teshera Sterne and Richardson May 2011 and Wingscapes Timelapse Camera User Guide 2010 Added reference panel description from Andrew Richardson 1 01 Oct 2012 Geri Tie
55. each file that the name you created matches the standardized template PARK H YYYY mm dd HHMMSS OR PARK YYYYmmdd HHMMSS 8 Press the Rename button 9 After verifying that the files were renamed properly delete the duplicate versions created in Step 1 ao rf 231 SOP 11 Data Management and Quality Assurance Quality Control Appendix 11 B Using Bulk Rename Utility software continued Computer files record the date time they were Created and Modified in their properties A file s Created Date is modified each time it is copied moved The Modified Date is updated when a file is opened Since in almost all cases the files have been moved from the recording equipment s chip to a computer for renaming the Modified Date not the Created Date is used to establish when the recording was made The file name should include the date time that the recording started Since the file is created by the Olympus recorder when the file is closed and saved we must subtract the length of the recording from the Modified Date in order to obtain the start time for Olympus files only Please refer to your deployment field sheet for each site to determine the programmed length of recording 232 SOP 11 Data Management and Quality Assurance Quality Control Appendix 11 C Instructions for transferring images to the PhenoCam Server via FTP Setting up a Site Before you can transfer files your site must be set up with the P
56. filenames park staff must rename raw image files immediately after their collection from field units Instructions on how to use the free Bulk Rename Utility software are provided in Appendix S11 B This format is compatible with the PhenoCam Image Processor program Raw image files from automated cameras are assigned names as follows PARK YYYY MM DD HHMMSS jpg Where PARK the four letter NPS acronym corresponding to the park of deployment e g ACAD H the four digit site number assigned by USA NPN for the site of deployment YYYY MM DD HHMMSS the date time of data capture year month day hour minute and second Audio files During preparation for deployment both Song Meter and Olympus ARU s are customized with site identification numbers as described in the Deployment and Maintenance of ARUs SOP Song Meter ARUs assign filenames automatically using this site prefix PARK entered by the user However Olympus ARUs cannot be programmed to assign sufficient custom filenames 225 SOP 11 Data Management and Quality Assurance Quality Control and Olympus files must be renamed as soon as possible after collection Olympus files are created with an 8 digit name consisting of 0001 where is the site prefix entered as the four digit site number assigned by USA NPN followed by a four digit number corresponding to the sequence in which the file was recorded As soon as possible after data collection park st
57. files Templates for storing templates Results for storing results Archives for storing clips of the original recordings for historic or verification purposes O O OO Within the Surveys directory create a directory for each location that you are monitoring For example all recordings collected at SARA e g SARA0001 SARA0002 SARA0003 SARA0004 are stored in a folder named SARA Note that each site is identified by the four digit number assigned to the site by USA NPN and thus the site numbers will not be as simple or sequential as those shown in this example If you are using the MySQL database the location folder names should match those in tblLocation fldLocationName Within the Templates directory create a directory for each species that you are monitoring Use a coding scheme that allows you to rapidly find what you are looking for For example three templates for birds can be named SOSP for Song Sparrow BTNW Black throated Green Warbler and OVEN Ovenbird If you are using the MySQL database the folder names should match the field tblSpecies fldSpeciesCode Other folders directories will be created by R as you work through the analysis For long term monitoring projects these directories may be created on separate drives or across a RAID system redundant array of independent disks All data must be redundantly backed up While storage on a raid does place the data in two locations a separate backup drive is also
58. for details see the Olympus instruction manual The files containing the recording schedule for Song Meter units can be left on the card if you wish to use the same schedule or it can be erased and replaced with a new schedule Be careful about reusing schedules that contain specific start and stop dates rather than those set to record a certain amount per day as they will not be reusable File Types The files from the Olympus units are recorded in MP3 format while the files from the Song Meter are WACO format developed specifically by Wildlife Acoustics The MP3 is a lossy compressed file format meaning that some audio data is thrown out for the sake of smaller files sizes when compression is performed WACO is a lossless compressed file format and does not lose any information in the process of compression but results in a larger file size than the MP3 format Different audio software may require different formats in order to play view and manipulate audio data so it may be necessary to convert these files into different formats Converting Files Olympus MP3 files can be converted to other formats using free downloadable audio software One option is called Audacity which can be downloaded at http audacity sourceforge net and another option is RealPlayer which can be downloaded at http www real com Song Meter WACO files can be converted to WAV files using free Kaleidoscope software available for download on the Wildlife Acousti
59. g Operations Privileges Routines Events gt Triggers s 0 Table Action Rows Type Collation Size Overhead Recent tables tbicard T Browse Structure 3 Search F lt insert Empty amp Drop 12 Xeround latint_swedish_ch unknown tbleardrecorder Browse Structure Search 3 lt Insert GF Empty amp Drop 12 Xeround latini_swedish_ci unknown tbllocation M Browse Structure S Search F Insert Empty Drop 12 Xeround latini swedish ci unknown F Gece thipareon _ Browse z Structure Search F Insert Empty Drop 12 Xeround latini_swedish_ci unknown tbllocation tbipersoncontact Browse Structure Search Insert Empty Drop 12 Xeround latini_swedish_ci unknown E tbiperson tbipriors _ Browse Structure Search J Insert Empty amp Drop 12 Xeround latin _swedish_ce unknown Sea tbiprogram Browse Structure Search J Insert Empty Drop 12 Xeround laint_swedish unknown E tbiprogram J tbirecorder _ Browse Structure Search 3 Insert GF Empty amp Drop 12 Xeround latini_swedish_ci unknown _ tbirecorder tbiresult T Browse Structure amp Search je Insert G Empty Drop 12 Xeround latini_swedish_ci unknown m ces thispecies T Browse Structure Search lt Insert Emory Drop 12 Xeround latint_swedish_ci unknown m tbisurvey tbisurvey Browse Structure Search F insert GF Empty Drop 12 Xeround latini_swedish_ci unknown thitempiate thitemplate J Browse Struc
60. http download cnet com WV Player formerly Wav Player 3000 2139_4 10472299 html and SoX at http sox sourceforge net A package is a set of functions that runs in R 120 SOP 7 Acoustic Template Creation Terminology Bandpass filter An audio filter that trims frequency data from above and below the frequency band that is allowed to pass through In the digital implementation here we specify a minimum and maximum frequency that we want to pass through and all frequencies below the minimum and above the maximum are discarded Binary point matching A method for sound detection in which the acoustic template is converted to a matrix of on and off cells The mean amplitude in decibels of the corresponding on points at each time interval in the survey is compared to the mean amplitude of the corresponding off points The user specifies a minimum acceptable difference between the two values to limit the results and local maximum difference values above the minimum value identify events MP3 A lossy compression file format engineered to preserve the most audible human speech frequencies The compression process has a number of components and the degree of information loss is determined by how much information must be trimmed to meet the target file size per second minimum size is 128kbps MP3 files are low pass filtered above the threshold of human hearing and occasionally low amplitude freque
61. is specified or where the default is not the desired value At the minimum you must specify the wav clip to use which can either be a quoted file path or an existing wav object read in using tuneR s readWave or readMP3 functions Optionally you may identify the start and end of the clip in seconds if planning to use only a short segment of a longer file change the frequency limits in kHz identify the selection method choose either click rect auto or line see descriptions and examples that follow and identify how dense the points within the template will be with the click selection method use the default of dens 1 for other methods if dens 1 all points within the selection area will be saved and for dens less than 1 only the specified proportion of points will be chosen e g dens 0 2 will save roughly every fifth point dens 0 5 will save roughly every other point etc A new window will open to display the spectrogram of the chosen clip Time is labeled along the X axis and frequency is labeled along the Y axis The spectrogram is a matrix of time and frequency bins and the corresponding bin numbers are labeled along the secondary X and Y axes If the selection method is set to click you will be prompted to select individual points to include in the template Do this by hovering your mouse over the points you intend to select and left clicking each point Right click to end the selection proce
62. is the location of the directory to move files to Example C Acoustics Surveys include the apostrophes as this is a text string csv dir This is the location of the directory that will store the csv file that summarizes the file information This defaults to the destination folder for the recordings surveys or you can specify a new directory such as C Acoustics Surveys include the apostrophes as this is a text string csv name This is the name of the csv file that summarizes the file information If you do not choose a name the assigned name will be the loc prefix and the date the files were copied ina YYYY MM DD format LOCA0001 20121109 csv duration This is the duration in seconds of the surveys to extract mins between This identifies the number of minutes to leave between each survey index This can be set to hour or time0 Hour extracts surveys from the top of each hour and time0 extracts surveys starting at the beginning of the recording kbps Most mp3 files are compressed to a constant bitrate SOP 6 Deployment and Maintenance of Autonomous Recording Units defines the bitrate to select as 128 kbps samp rate The sampling rate of the mp3 file The Olympus recorder in SOP 5 Building an Autonomous Recording Unit defaults to 44100 Hz channels stereo 2 mono 1 The Olympus recorder in SOP 5 can only record in stereo 164 SOP 8 Automated Sound Detection and Classification Upload survey metadat
63. left call 2 after raising amp cutoff to 31dB dens 1 and buffer 2 The off points are all at least two time and or frequency bins away from the on points Top right call 3 after raising amp cutoff to 31dB dens 0 8 buffer 0 after on and off point selection Bottom left call 3 after raising amp cutoff to 31dB dens 0 2 buffer 2 Bottom right call 4 after raising amp cutoff to 31d0B dens 0 8 buffer 2 select auto 137 SOP 7 Acoustic Template Creation Call 5 demonstrating the click selection system TNW_click_d100_B lt makeBinTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav t lim c 0 2 8 frq lim c 2 9 select click wW 20 40 60 80 100 120 20 40 6o 80 100 120 9 i L 9 L fi l L 480 H 180 8 8 _ gt a b 160 ENa AT a R TE H 160 g A qg 17 AC Ae R 140 140 x 2 Z 64 65 2 m 120 8 H 120 v v 2 5 4 3 54 3 100 F m 100 E gd L 80 447 H 80 3 60 37 shoe Pas 60 2 T T T T T 2 T T T T T 0 5 1 1 5 2 2 5 0 5 1 1 5 2 2 5 Time s Time s Figure S7 7 Left call 5 with binary FALSE and select click on point selection is done by choosing individual points one at a time Right call 5 after right clicking to stop on point selection off point selection is done one point at a time as well Binary Point Templates From Multiple Songs It is possible to create a template from two example songs to b
64. left if the signal is preferable in the right channel It is not necessary to have a mono template but the left channel is used by default Correlation Templates There are two template matching algorithms in this package correlation matching and binary point matching The template building process is very similar for both of these algorithms but the template structure is quite different When building a correlation template you will interactively define the boundary of the template in the spectrogram effectively making a finer choice of time boundaries and applying a band pass filter at the same time The template defines not only where you want higher amplitudes in the spectrogram but also where you want low amplitudes Be sure to include both in your selection Some of the methods below allow selection of multiple regions within the spectrogram so the final selection need not be a rectangle When choosing what low amplitude regions to include in the template a good place to begin is to consider what songs or noises might overlap the spectrogram you are working with and specifically include those regions as low amplitude areas Create SCC Templates From Sound Clips makeCorTemplate The arguments to makeCorTemplate can be viewed with the args command gt args makeCorTemplate function clip t lim NA frq lim c 0 12 binary FALSE select 1 buffer 0 spec cols gray 2 col sel 99009975 orange
65. m The microphone is inside a windscreen made of wire mesh and faux fur The microphone can be visually inspected by holding the base the plate as Figure 6 3 Hanging close to the windscreen as possible and gently and slowly rocking the microphone inside wire windscreen while pulling it directly off the base It may help to adjust mesh and faux fur your grip on the base and the windscreen several times by rotating the base 96 SOP 6 Deployment and Maintenance of Autonomous Recording Units Each ARU is enclosed in a weather proof Pelican case with a 3 5mm 1 8 mic input jack on the bottom Pull the case tight against a tree or post by using plastic cable ties The cable ties pass through the handle on the left side of the case and the steel bar on the right side of the case Install an upper chain and a lower chain In addition to the plastic cable ties install a length of vinyl covered steel rope through the same points around the tree and then fasten it with a cable clamp for security prn A pinnu i i i Figure S6 4 Pelican weatherproof case attached to tree Once the ARU is firmly attached to the tree or post plug the microphone into the jack on the bottom Arrange the wire so that it falls as close to the trunk as possible descends below the mic input jack and then loops once before plugging into the jack The hanging loop will serve to allow water to drip off the wire before it enters the inpu
66. most audible human speech frequencies The compression process has a number of components and the degree of information loss is determined by how much information must be trimmed to meet the target file size per second minimum size is 128kbps MP3 files are low pass filtered above the threshold of human hearing and occasionally low amplitude frequency data are discarded if they occur simultaneously with high amplitude frequencies MP3 files save considerable storage space versus uncompressed files but obligatory decompression time can be substantial Spectrogram cross correlation A method for seeking a known template in a survey consisting of unknown songs The correlation of amplitude values in the FFT template matrix to a matrix in the survey is measured using the Pearson method The survey matrix then shifts one time bin and the correlation to the template is measured again The user specifies a minimum Pearson score and local maximum scores identify events Survey A recording that will be searched for the template Must be a WAV or MP3 file and must be longer than the template Template A recorded song example which will provide the search image for the computer Must be a WAV or MP3 file A template may differ from a simple song clip by retaining bandpass filter values and score cutoff values WAC The Wildlife Acoustics proprietary compression format Use of this format is restricted to Wildlife Acoustic s Song Meter recording u
67. name lt strsplit recorderName 2 1 l l remove fil survey name fileNam recorderName 1 _ lt paste F users jkatz3 Results 20120912_ sccDetect templat file name fileName Revision History surveyName sep L templates survey survey Version Date Revised by Changes Justification 0 10 Sept 2012 Jon Katz Intial draft 0 20 Dec 2012 Jon Katz Added binary point matching additional sections 0 30 Jan 2013 Geri Tierney Separated document into SOPfor 1 Audio Brian Mitchell Detection and for 2 Template Creation Editorial and formatting changes 0 31 April 2013 Brian Mitchell Provided background information regarding Response to Geri Tierney Song Scope and the decision to pursue an R external 1 00 May 2013 Jon Katz Geri Tierney based analytical approach review Added text for Appendix C on downloading and installing R Minor edits for clarit Accepted changes by BM and GT Replaced figure in Appendix A Added mp3 subsample procedure Formatting changes Added survey subsampling procedure for mp3 files 180 Appendix S8 A Creating a MySQL database MySQL As with most investigations it is preferable to store information about the project including the project data in a relational database There are several advantages to this including 1 reduction in errors 2 ability to have multiple users access the same database and
68. needed since failure of a RAID controller can prevent access to all data on the RAID system Download Recordings From SD Card R becomes involved in the analysis process when an SD card or other media device is plugged into a computer to download the recordings The first step of moving the recordings from the card to the computer is handled by the fileCopyRename function The procedure varies depending on whether the survey recordings are in wac format versus wav or mp3 format The database will enforce associations between the results and the surveys locations cards recorders and analysts The connection to the survey will be automatic but the connection to the other attributes of the monitoring program requires that the user specify the card and recorder that the results stem from by identifying the value from tblCardRecorder pkCardRecorderID Therefore the value for the CardRecorderID will need to be known when downloading surveys from the SD cards The simplest way to look this up is to use the query that downloads a table of 161 SOP 8 Automated Sound Detection and Classification relevant CardRecorderIDs This query will download all CardRecorderIDs for specified sites within a specified time window Download a table of CardRecorderIDs that correspond to site and time associations crlocs lt dbDownloadCardRecorderID db name UVMacoustics date deployed 0000 00 00 date collected 0000 00 00 loc prefix c MABIO1
69. o It will help to quickly scan through the photo data beginning mid season and end to ensure that the camera view did not shift and lose part of the focal area o If recording data from a partial individual e g a tree branch make sure this is recorded in Nature s Notebook o Start with the photo taken as close to noon as possible on the first day of monitoring If that photo is blurry or dark use the closest photo to noon that allows you to see the plant phenology o If the filmstrip view does not allow you to see phenophases adequately double clicking on the image thumbnail at the bottom of Windows Explorer will open the default photo program on your computer that program should allow you to zoom in on sections of the photo Literature Cited Sonnentag O K Hufkens C Teshera Sterne et al 2012 Digital repeat photography for phenological research in forest ecosystems Agricultural and Forest Meteorology 152 159 177 Revision History Version Date Revised by Changes Justification 1 00 May 2012 Geri Tierney Adapted from Digital repeat photography for Andrew phenological research camera deployment Richardson and image processing protocol Sonnentag and Richardson June 2011 and Digital repeat photography for phenological research in forest ecosystems Sonnentag et al 2012 1 01 Oct 2012 Geri Tierney Added procedures for running PCIP software Michael Toomey 1 02 Nov 2012 Brian Mitchell Added procedures f
70. of birds seen If a plant is in flower then observers estimate and record the number of flowers and flower buds seen on that individual plant as one of several quantitative classes If frog calling is heard then observers estimate and record abundance within one of three classes 1 individuals can be counted there is space between calls 2 calls of individuals can be distinguished but there is some overlapping of calls and 3 full chorus calls are constant and overlapping For plants observations are made on marked individuals For animals observers look and listen for the target species during a walk along a designated transect through the site The standard search time will vary among sites as designated by park staff Automated Data Automated recording and digital time lapse photography are an important data source for long term phenological research providing a consistent and objective stream of data at optimal frequency in both accessible and remote locations Autonomous recording units ARUs may be 14 used to detect vocalizations of many species of interest including bird amphibian insect and bat species detection of these vocalizations is indicative of migratory and reproductive phenophases Two types of ARUs are deployed in participating parks 1 Song Meter recording units produced by Wildlife Acoustics Inc and 2 an inexpensive homemade ARU designed by Jon Katz and Corinne Brauer containing an Olympus digital recor
71. on first appearance data of butterflies Oecologia 156 227 235 Willis C G B R Ruhfel R B Primack A J Miller Rushing J B Losos and C C Davis 26 2010 Favorable Climate Change Response Explains Non Native Species Success in Thoreau s Woods PloS ONE 5 e8878 27 Revision History Version numbers will be incremented by a whole number e g Version 1 30 to 2 00 when a change is made that significantly affects requirements or procedures Version numbers will be incremented by decimals e g Version 1 06 to Version 1 07 when there are minor modifications that do not affect requirements or procedures included in the protocol Add rows as needed for each change or set of changes tied to an updated version number Revision History Log Version 0 00 1 00 1 01 1 02 1 03 1 04 1 05 Date July 2008 draft June 2010 draft Sept 2010 draft Oct 2010 draft Nov 2010 draft Dec 2010 draft April 2011 draft Revised by Geri Tierney Geri Tierney Abe Miller Rushing Brian Mitchell Fred Dieffenbach Geri Tierney Geri Tierney Geri Tierney Adam Kozlowski Geri Tierney Brian Mitchell Geri Tierney Changes Initial draft for APPA Expanded to encompass NETN Revised to Oakley et al standards Aligned with USA NPN protocol Description of pilot study SOPs for automatic recording and legal requirements included Starting in 2011 monitoring will include measure of
72. phenophase abundance Adjusted procedure for one time observation Updated goals and objectives Updated Appendix E and F Editorial changes Adjusted observation definitions to match NPN change Clarified upper limit on site size Clarification of legal requirements and collection of personal information Editorial comments Added Repeat Panorama SOP noted that availability of legacy data is preferable in species selection added priority habitat and ecotone language to objectives suggest parks focus on only 4 5 key species Added additional sections to match I amp M standards Oakley et al Adjusted list of SOPs to include automatic recording SOPs Inserted table of priority park habitats with selected key species Removed option for volunteer to choose custom site Adjusted number of sites per park habitat to be gt 3 and number of individual plants per site to be gt 3 Eliminated App B and added 29 Justification Program has expanded and developed Based on discussions at our Fall 2010 NERPN meeting Based on Brian s comments and discussions with Abe Miller Rushing and Fred Dieffenbach 1 10 1 20 1 21 1 22 1 30 Spring 2012 draft Sept 2012 Jan 2013 Jan 2013 May 2013 Geri Tierney Geri Tierney Geri Tierney Ellen Denny Geri Tierney Geri Tierney Brian Mitchell Ed Sharron App F Editorial changes Added sections describing automatic recor
73. responsible for inspecting their vehicles before every use to ensure the vehicles are in safe working condition This includes visually checking tire pressure adjusting mirrors and making sure equipment is secure as well as taking care of preventative maintenance in a timely manner It is strongly recommended that monitoring staff obey the following rules these rules are mandatory in government vehicles e Wear a seat belt e Do not use cell phones both talking and texting while driving e Adhere to all federal and state vehicle regulations including all posted speed limits Procedures for reporting a motor vehicle accident In the event of an automobile accident volunteers and NPS staff should follow NPS accident reporting procedures Cooperators or contractors would need to follow their organization s procedures The NPS procedures are as follows 1 Stop immediately and turn on emergency flashers 2 Take steps to prevent another accident at the scene 3 Call 911 or ambulance if necessary 4 Notify police NPS law enforcement if at a park with law enforcement ACAD MIMA MORR and SARA and the park Natural Resource Manager The park Natural Resource Manager will notify NETN staff 5 Inthe event of death actual or potential serious injury or significant property damage damage greater than 2 500 the staff involved must convey this information as soon as is practical to NETN staff so that the NPS Regional Tort Claims Off
74. s Time s 20 40 60 80 100 120 9 180 160 140 a 120 v Fe 2 100 ik 80 37 60 2 T T l 0 5 1 1 5 2 2 5 Time s Figure S7 1 Top left the initial spectrogram after calling makeCorTemplate before making any selections Top right call 1 after making a single rectangular selection Bottom call 2 after making two rectangular selections 127 SOP 7 Acoustic Template Creation Call 3 change the density to 0 8 BTINW_rect_d80_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav select rect dens 0 8 Call 4 change the density to 0 5 BTNW_rect_d50_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav select rect dens 0 5 Call 5 change the density to 0 2 BTINW_rect_d20_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav select rect dens 0 2 20 40 60 80 100 120 20 40 60 80 100 120 g l l l Pe l L 180 180 8 8 160 d 1 pe 7 n 140 ry 120 5 5 se 5 es 57 D D 100 E E gd 80 T 60 37 E 60 2 T T T 2 T T T T T 0 5 1 15 2 2 5 0 5 1 15 2 2 5 Time s Time s 20 40 60 80 100 120 m 180 m 160 x 140 x 6 2 120 3 5 D 100 re 80 3 60 Time s Figure S7 2 Top left call 3 after making one selection at a density of 0 8 Top right call 4 after making one selection at a density of 0 5 Bottom cal
75. sample rate BTNW_rect_d100_B Dropbox LabDemo Templates BTINW wav 24000 BTINW_rect_d100_b2_B Dropbox LabDemo Templates BTNW wav 24000 BINW_rect_d20_b2_B Dropbox LabDemo Templates BTNW wav 24000 BTNW_auto_d80_b2_B Dropbox LabDemo Templates BTNW wav 24000 BTNW_click_d100_B Dropbox LabDemo Templates BTINW wav 24000 lower frequency upper frequency duration on points BTNW_rect_d100_B 3 562500 6 703125 1 98 735 BTNW_rect_d100_b2_B 3 375000 6 703125 1 86 735 BTINW_rect_d20_b2_B 3 281250 6 656250 1 86 80 BTINW_auto_d80_b2_B 3 515625 6 703125 1 96 201 BTNW_click_d100_B 3 609375 6 656250 M73 71 off points score cutoff BINW_rect_d100_B 5472 9 0 BINW_rect_d100_b2_B 4639 8 5 BINW_rect_d20_b2_B 580 9 5 BTNW_auto_d80_b2_B 1232 8 5 BTNW_click_d100_B 81 7 0 Save Templates Save the Correlation Template list to a local disk The template list can be saved to a local directory with the writeCorTemplates function gt writeCorTemplates templates CORtemplates dir C Users jkatz3 Dropbox LabDemo WAVclips Templates Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWd1 0 ct Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWpartial ct Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWd 8 ct Template written to file C Users jkatz3 Dropbox LabDemo WAVclips Templates BTNWd 5 ct
76. sites are selected for phenology monitoring within each monitored habitat A site is the area which is searched for one or more monitored animal species and which encompasses selected plants of one or more species Typically sites are selected and setup by program staff or collaborators However in some cases volunteers may collaborate with park staff to identify sites that are both convenient and appropriate for monitoring An analysis of multiple sites and methods is underway at ACAD to help determine the best number of sites individual plants and automatic recorders for monitoring phenology in these parks The effects of sampling frequency on the detection and estimation of trend in phenology depends on the shape of the temporal distribution of the phenophase in question and the magnitude of the change that is actually occurring Miller Rushing et al 2008a Moussus et al 2010 Ideally monitoring every second day will maximize the ability to detect and accurately estimate change There is a substantial drop in the ability of data sets to reflect actual changes taking place when observations are made less frequently than once per week Miller Rushing et al 2008a Moussus et al 2010 Following USA NPN recommendations NETN observers are instructed to monitor sites at least weekly but ideally every other day when phenology is changing quickly such as in the spring and fall At most sites data from multiple observers is pooled to achieve opt
77. standard tripod nuts embedded in the camera case and can be mounted on a pole or stake using the Wingscapes outdoor camera mounting bracket see above under Camera housing and accessories or on a tripod or strapped to a tree Connecting webcams For webcams plug the ethernet and power extension cables into the ports on the camera and into the site s power supply and LAN router Check to make sure the camera is on Then install the webcam software tools for your model on your computer Check to see if the camera is detected and note the camera s IP address Enter this IP address into your internet browser s address bar a page should load with a blue background and a live image from the camera Depending on your network the IP address assigned to the camera may change periodically if this happens re run the webcam software tools program to verify the IP Specific instructions for connecting the Stardot NetCam SC are provided by the PhenoCam network in PhenoCam Installation Instructions by Cory Teshera Sterne et al updated April 2012 available at http phenocam sr unh edu webcam tools For StarDot webcams the ethernet must be plugged in before the power cable 207 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras Deployment metadata When a camera is deployed collect camera metadata documenting the camera site target image and setup as shown in Appendix S9 A Use the camera serial number to un
78. such as the Wingscapes models typically incorporate weatherproof housing as part of the unit If so no additional housing is needed Despite being designed for outdoor use outdoor webcams will likely need additional weatherproof housing installed Pilot testing successfully used inexpensive Vitek VT EH10 camera enclosures approx 25 The Wingscapes outdoor camera mounting bracket approx 10 is useful for mounting Wingscapes plant cams Wingscapes PlantCams use external SD memory cards and batteries 4 AAs for TimelapseCam This SOP recommends using rechargeable batteries high capacity batteries should last approximately one month At high resolution the WSCA04 will store 750 photos per GB enough for 15 days per GB if photos are taken every 30 minutes around the clock The WSCTO1 will store about 450 photos per GB at its highest resolution for about 10 days per GB Therefore a 4 GB card should be sufficient to match the maximum deployment length with AA batteries For longer deployments a solar power option is available from Wingscapes about 80 Aiming and mounting the camera Cameras are used to monitor individual plants as well as vegetation canopies Images from individual plant monitoring are analyzed for leaf greenness and or flowering phenophases For monitoring individual plants the camera is aimed at the plant or plants of interest of a species selected from the park s list of monitored species in a particular habitat
79. the same technique to wrap the wire around the pin Repeat A nearly invisible trace barely visible for the second microphone using the remaining free on the left pin pictured above conductors After both microphones are soldered in place Connects ME MICOPRONE pit 10 the Ea aluminum housing Separate the shield test for connectivity between all connections and then use lead into a pair of leads and move to a thin layer of waterproof glue to insulate and stabilize the the outside of the insulated connections Avoid applying glue to the fabric face of the microphones NOTE This step would not be needed for PA3 microphones but the microphones should be attached to each other and oriented away from each other and stabilized with glue When the glue dries snugly wrap a cable tie around the audio cable 2 5 above the microphone This will keep the plate from slipping down the cable On the opposite end of the audio cable slide the housing for ee er geese i e microphones after soldering e the male audio connector onto the wire Solder a phono plug Zjuminum housings connec ed Oihe to the wire following the same procedure as for the pole take care to prevent short circuits and be sure to match the microphone polarity with the proper conductor 87 SOP 5 Building an Autonomous Recording Unit previously assembled internal connector NOTE For the PA3 microphones at this step you would attach the RCA to 3 5 mm p
80. to block out regions of points to be on points and make other blocks of regions to be off points This approach will select all points above the amplitude threshold and within the initial blocks to be on points and all points below the threshold and within the appropriate blocks to be off points Call 2 two Song Sparrow clips using click selection SOSP_rect_d80_b3_midphrase_B lt makeBinTemplate2 clip L list s6 home jkatz3 Dropbox UVMacoustic Analysis bird Recordings s6 wav s7 home jkatz3 Dropbox UVMacoustic Analysis bird Recordings s7 wav t lim L list c 1 4 4 5 c 1 4 1 select rect buffer 3 dens 0 8 amp cutoff 31 name SOSP_rect_d80_b3_midphrase_B To enable rectangular point selection we use the same command as above but change the argument for select to rect In this call the amplitude cutoff is explicitly defined to save time but the time shift procedure must be repeated as above Specifying a buffer of 3 prevents any off point from being within 3 time or frequency bins proximity to a signal point regardless of whether the signal exist in both clips Setting dens 0 5 reduces the number of points selected in the matrix and roughly half of the available points will be saved When it is time to select on cells you should see this prompt in the R gui Rectangular selection Select upper left corner of on rectangle with a left click Right click to exit After left cli
81. to potential hazards Obey all traffic laws and speed limits Adjust speed to changing weather or traffic conditions Allow adequate following stopping distance Avoid distractions such as eating while driving Be alert for pedestrians or bicyclists using roadways Be watchful for wildlife crossing roads especially at early morning dusk and after dark Do NOT drive if fatigued Stay alert 59 SOP 1 Safety Appendix S1 C Safety Forms Safety Acknowledgment Form By signing below I certify that I have read the safety section of the Volunteer Training Manual and the Phenology Monitoring Job Safety Analysis I have shared any safety concerns or suggestions with the park Natural Resource Manager and they have been addressed to my satisfaction Print Name Signature Date Please return this form along with the completed and signed NPS Agreement for Individual Voluntary Services to the park Natural Resource Manager These forms only need to be completed once for each volunteer prior to any field monitoring activities An annual review of the Volunteer Training Manual and Job Safety Analysis is recommended for all volunteers 61 SOP 1 Safety Appendix S1 C Safety Forms continued Phenology Monitoring Safety Checklist One month to one week before field work Complete volunteer form and JSA acknowledgment and return to park Natural Resource Manager one time requirement Contact park Natural Res
82. volunteer observers Deployment maintenance and data collection from automated recording devices may be performed by network staff cooperators or park staff or volunteers depending on staff availability and volunteer abilities Trained volunteer observers provide the majority of labor making observations and submitting data online and in some cases may assist with other tasks Qualifications At the network level a program leader overseeing program coordination and data analysis needs a background and experience in ecological field methods and data analysis and should have hands on experience collecting data using this protocol In order to provide training the NETN Science Communication Specialist must be familiar with the specific methods used herein and have experience explaining scientific concepts to park volunteers The NETN Data Manager should become familiar with the USA NPN database and interface as well as the legal requirements pertaining to this dataset At the park level a coordinator at each participating park or APPA region must have good working knowledge of park habitats and the specific species monitored by this protocol Park coordinators must be able to confirm correct identification of all monitored species Ideally park coordinators would also have experience organizing park volunteers Deployment maintenance and collection of data from automated recording devices requires some level of technical ability and familia
83. wav sep You can then save the keys individually using a similar loop for i in l length event recStimes write csv event recStimes i 178 SOP 8 Automated Sound Detection and Classification file paste E users jkatz3 Desktop SARA3_A_062610_ names event rec times fi csv sep Or aggregate them and save a single master key event key lt rbind fill event recStimes write csv event key E users jkatz3 Desktop SARA3_A_062610_key csv Batch Analysis To make batch analysis easier you should plan ahead with your file management when you download field recordings Use the file management structure outlined at the beginning of this document in which all recordings are aggregated by recorder within a directory for the date of download Imagine all recordings from the SD cards are in a directory named 20100510 which is a date in the format YYYYMMDD Within this directory are four more folders containing the survey recordings from each recorder These directories are named after each site SARAOOO1 SARA0002 SARA0003 SARA0004 For batch analysis use sccDetect which calls sccCor and findPeaks and then writes out the results as a series of csv files The steps the for loop needs to complete are 1 create a list of recorders 2 loop through the list of recorders creating a list of surveys for each recorder 3 loop through the list of surveys read
84. while in the field staff must notify the RM DI immediately At the end of the day staff must notify the RM DI that they have returned from the field At ACAD the SPOT Messenger can be used to notify NETN that more time is needed in the field or that field work is completed NETN staff will relay this message to the RM DI If NETN staff are not contacted they will assume that the monitoring staff checked in directly with the RM DI 39 SOP 1 Safety Monitoring staff are responsible for being aware of the time and ensuring that end of day check ins occur on schedule the RM DI will call emergency services if the monitoring staff misses their check in and cannot be located within 30 minutes of the check in time At designated accessible sites on or near a trial it is not necessary to contact the RM DI on each monitoring day for check in check out However all monitoring staff must notify a trusted person spouse friend co worker etc of their whereabouts during monitoring activities and that person must be given contact information for the RM DI in case of an emergency Personal Gear Monitoring staff are responsible for ensuring they are wearing field appropriate clothing and footwear such as long pants a hat and hiking boots Depending on the weather rain gear or warm clothing should be taken into the field and it is recommended that an extra set of clothing be kept in the vehicle Monitoring staff should take care to avoid over ex
85. will be compromised by storm conditions If you see or hear a thunderstorm coming retreat from high ground and exposed areas Go inside a sturdy building or vehicle if possible If you can t get inside and if you feel your hair stand on end lightning is about to strike Make yourself the smallest target possible and minimize contact with the ground Crouch down on your pack on the balls of your feet and keep your feet close together Place your hands on your knees and lower your head During a thunderstorm members of the crew should stay separated by at least ten feet Poisonous plants Contamination toxicity from contact Learn to identify poison ivy in its many growth especially poison with poisonous plants forms ivy Wear long sleeves and pants Be aware of poison ivy and avoid coming in direct contact with it Thoroughly wash hands equipment and clothes with Tecnu or similar specialized soap if you come into contact with poison ivy Working in bear Black bear encounter Be especially alert near dawn or dusk territory Be especially aware of mother bears with cubs Never approach cubs or come between a mother bear and her cubs Face the animal continually make noise do not freeze or remain silent Appear larger by standing tall waving arms or jacket over your head Slowly back away do not approach a bear Never run from a bear Throw things and shout loudly Fight back aggressively 56 SOP 1 Safety Appendi
86. with USA NPN s NCO staff to obtain any updated procedures or online interface February Begin field season planning Update methods and training materials Schedule training sessions March Park coordinators visit designated sites and update marking Deployment of automated recording devices may occur Monitoring by automated devices and returning observers may begin April June A training session occurs at each participating park and APPA region Monitoring by automated devices and observers continues Observers submit data online into Nature s Notebook July November Monitoring by automated devices and observers continues Observers submit data online into Nature s Notebook Park coordinators solicit feedback from 21 volunteer observers NETN Data Manager obtains park dataset from USA NPN database Annual operational review occurs and protocol is updated as needed e December Data analysis is underway Equipment and Supplies Phenology observation by monitors requires only plant marking equipment at parks allowing volunteers to select and mark plants and information and data sheets available for download online at the Nature s Notebook website In addition a clipboard may be helpful and binoculars are recommended for some phenophases such as leaves or birds high in trees Downloading data sheets and online submission requires access to a computer with an internet connection Most volunteers will have
87. x Table A 5 Monitored phenophases for amphibians Siopneds E Spring peeper Wood frog Adults on land x x x Adults in water x x x Adults feeding x x x Vocalizing x x Mating x x Fresh eggs x x x Dead adults x x x 32 Table A 6 Monitored phenophases for birds Red White Great Praprese Ovembld Bobol winged roe rented Tron pach Active individuals x x x x x x xX Feeding x x x x x x x Fruit seed x x x x consumption Insect consumption x x x x x Flower visitation Nut gathering Calls or song Xx x x x x x x Singing males X x x x x Mating x x x x x x x Nest building X x x x x x Dead individuals x x x x x x Xx Individuals at a x x x x x x feeding station Table A 7 Monitored phenophases for Insects Lepidoptera USA NPN Phenophase caterpillar butteniiy Active adults x x Flower visitation x Migrating adults Xx Mating x x Active caterpillars x x Caterpillars in tent x Caterpillars feeding x x Dead caterpillars x x Dead adults x x Individuals at a feeding station x Individuals at a light x Individuals in a net x x 33 Appendix B NETN Phenology Program Contact List NPS contacts Park Network Name NETN Brian Mitchell NETN Abe Miller Rushing NETN Ed Sharron NETN Adam Kozlowski NPS Margaret Beer ACAD Bruce Connery ACAD David Manski ACAD Bill Zoellick ACAD Jonathan Gormley ACAD Seth Benz APPA Fred Dieffenbach APPA Casey Reese APPA John Odell BOHA SAIR Marc Albert
88. 0 BINW_rect_d80_C Dropbox LabDemo Templates BTNW wav 24000 BINW_rect_MandHnotes_C Dropbox LabDemo Templates BTNW wav 24000 lower frequency upper frequency lower amp upper amp BTNW_auto_d100_C 3 516 6 750 94 710 0 000 BTNW_auto_d20_C 3 516 6 750 81 874 217993 BTNW_auto_d80_C 3 516 6 703 81 843 3 428 BTNW_click_allNotes_C 1 359 9 562 76 263 3 203 BTNWlineO L359 9 797 78 076 4 641 BTNW_line_d100_C 1 641 10 078 86 965 2 814 BTNW_rect_C 3 141 7 453 86 965 0 000 BTNW_rect_d20_C 2 29 18 Te219 83 995 5 877 131 SOP 7 Acoustic Template Creation BTNW_rect_d50_C 2 953 7 547 82 282 2 098 BTNW_rect_d80_C 3 234 7 078 82 282 2 098 BTNW_rect_MandHnotes_C 2 250 8 719 89 012 0 000 duration n points score cutoff BTNW_auto_d100_C 1 963 6510 0 41 BTNW_auto_d20_C 1 920 744 0 35 BTNW_auto_d80_C 1 963 1645 0 40 BTNW_click_allNotes_C 2 347 197 0 41 BTNWlineO 2 091 967 0 42 BTNW_line_d100_C ye 2209 0 29 BTNW_rect_C Zh 55 9486 0 40 BTNW_rect_d20_C 1 984 1088 0 42 BTNW_rect_d50_C 1 963 2350 0 38 BTNW_rect_d80_C 2 048 2058 0 41 BTNW_rect_MandHnotes_C 2 347 7629 0 45 Binary Point Templates From a Single Song The second type of template is a binary point template The building process is similar to that for correlation templates but the template structure is different binary point templates do not contain amplitude information from the song clip used to build them Instead the template provides coordinates of w
89. 0 579 0 663 0 597 0 604 0 690 s7 0 607 s7 0 634 0 647 0 500 0 510 0 672 0 575 0 926 0 571 0 505 0 600 0 543 0 659 0 518 0 609 0 639 0 533 0 599 0 677 0 637 0 606 0 599 0 632 0 572 s8 0 612 s8 0 595 0 662 0 563 0 605 0 603 0 629 0 575 0 927 0 578 0 661 0 627 0 631 0 535 0 618 0 567 0 565 0 565 0 620 0 548 0 656 0 544 0 561 0 645 s9 0 653 s9 0 586 0 694 0 670 0 620 0 651 0 652 0 526 0 630 0 920 0 772 0 828 0 647 0 648 0 708 0 540 0 563 0 528 0 659 0 562 0 727 0 570 0 614 0 710 s10 0 715 s10 sll s12 s13 0 689 0 623 0 706 0 581 0 768 0 719 0 805 0 611 0 691 0 749 0 584 0 555 0 675 0 638 0 591 0 502 0 742 0 700 0 793 0 586 0 740 0 707 0 672 0 592 0 620 0 557 0 654 0 526 0 687 0 645 0 640 0 541 0 766 0 821 0 609 0 645 0 975 0 822 0 726 0 619 0 834 0 921 0 671 0 684 0 741 0 686 0 933 0 587 0 636 0 652 0 565 0 836 0 814 0 737 0 745 0 586 0 593 0 574 0 702 0 538 0 646 0 591 0 621 0 566 0 570 0 533 0 654 0 525 0 745 0 700 0 797 0 593 0 634 0 585 0 683 0 555 0 815 0 764 0 691 0 623 0 646 0 597 0 669 0 546 0 688 0 646 0 730 0 565 0 727 0 746 0 695 0 621 sll s12 s13 0 689 0 693 0 591 s14 0 678 0 796 0 626 0 598 0 742 0 650 0 606 0 639 0 670 0 805 0 730 0 749 0 579 0 889 0 624 0 604 0 588 0 771 0 654 0 778 0 667 0 699 0 752 s14 0 691 s15 0 636 0 677 0 540 0 554 0 712 0 637 0 636 0 594 0 516 0 612 0 575 0 732 0 536 0 627
90. 0 631 0 701 0 853 uoneoly oduwa L onsnooy 4 dOS s23 0 688 SOP 7 Acoustic Template Creation This process could be repeated using various bandpass filter values and or various amounts of leading and trailing noise 153 SOP 7 Acoustic Template Creation Revision History should be spot checked to ensure they closely match the original 155 Version Date Revised by Changes Justification 0 10 Sept 2012 ___Jon Katz Initial draft as part of Audio detection SOP 0 20 Dec 2012 Jon Katz Added additional sections as part of Audio detection SOP 0 30 Jan 2013 Geri Tierney Separated document into separate SOP Brian Mitchell Editorial and formatting changes 0 31 April 2013 Brian Mitchell Added info to Introduction regarding why we Response to Geri Tierney are not using Song Scope and briefly external review describes the approach used Editorial changes 1 00 May 2013 Jon Katz Replaced references to Audacity with a new Audacity is no Geri Tierney function viewSpec accepted changes made by longer necessary BM and GT Formatting changes 1 01 May 2013 Brian Mitchell When changing the sample rate spectrograms changeSampRate appears to work well but testing was limited SOP 8 Automated Sound Detection and Classification Northeast Temperate Network Version 1 00 Introduction Read Me First There are a variety of tools available for automatic detection of species on audio recordings Among
91. 1 Pelican case weatherproofin gand protection 2 Battery pack with 4 D Cell batteries power supply 3 DM 420 Digital Voice Recorder audio recording device 4 SD Card data storage 5 Wire leading to external microphone Display screen On Off OK Menu DIGITAL VOICE RECORDER DM 420 Figure S6 2 The Olympus DM 420 Recorder The Olympus DM 620 recorder looks somewhat different 94 SOP 6 Deployment and Maintenance of Autonomous Recording Units Before you go into the field Calibration of Units If an Olympus ARU will be deployed using a microphone built from component parts as currently described in the SOP 5 Building an Autonomous Recording Unit the microphone must be calibrated to ensure that variation in the fabrication steps e g soldering ability does not affect performance Methods are currently being developed for testing and calibrating microphones before deploying them in the field This will ensure microphone recording quality and uniformity so that a network of mics is always surveying the same basic area and that replacing a mic in the event of equipment failure or other operational needs will not impact results A preliminary outline for microphone calibration is 1 Play back low and high frequency test sounds using a dB meter to ensure a specified volume at 1 m and 10 m 2 Record the test sounds at those distances and determine how closely the mic meets the exp
92. 3 10 category minus the days within the prior interval divided by two and then rounded down to the last whole number For each animal species monitored at a site estimate phenophase underway as the first date that abundance is recorded as any number gt 3 minus the days within the prior interval divided by two and then rounded down to the last whole number Estimate error as the prior interval divided by 2 For example if the second abundance category recorded on day 8 was preceded by the first abundance category recorded on day 7 the underway date is day 8 if the second abundance category recorded on day 8 was preceded by the first abundance category recorded on day 6 the underway date is day 7 and if the second abundance category recorded on day 8 was preceded by the first abundance category recorded on day 5 the underway date is still day 7 Phenophase end date For each individual plant or animal species monitored at a site estimate phenophase end date as the last date recorded as yes plus the days within the next interval divided by two and then rounded down to the last whole number Estimate error as the next interval divided by 2 Next interval refers to the interval between the current visit and the next visit For example if yes recorded on day 7 was followed by no recorded on day 8 the end date is day 7 if yes recorded on day 6 was followed by no recorded on day 8 the end date is day 7 and if yes
93. 5 more efficient when using a 12V battery source To use an external power supply on an SM2 set the power selection jumper to external When using an external power supply other than the SM2PWR by Wildlife Acoustics it is extremely important to make sure it has it has reverse polarity protection or to match polarity of the cable to the battery The positive terminal and the negative terminal should be marked and matched on both the cable and the battery The SM2PWR external power supply cable provides reverse polarity protection but not all other cables do Failure to connect the external battery properly will likely destroy the voltage regulator the SM2 motherboard or both The choice of power source and sampling rate depends on several factors including target taxon remoteness of recorder season and phenophases of interest see Table S6 1 At a minimum units should be set to record with lossless compression i e WACO format for 10 minutes at the top of every hour e g 8 00 to 8 10 this schedule incorporates the USGS Terrestrial Wetland 101 SOP 6 Deployment and Maintenance of Autonomous Recording Units Global Change Research Network TWGCRN suggested schedule of 5 min hour while allowing for a delay in startup of Song Meter units of 30 60 seconds Audio files may be subsampled after collection to yield standardized 5 min hr samples for analysis The recommendations in Table S6 1 are intended to be conserva
94. 7 SOP 11 Data Management and Quality Assurance Quality Control 0ccccccesceeeeereeeeeee 223 SOP 12 Data Analysis and REPOrin Gs cj25 4c25 cui nese ass ocala haa sued cael Jala Sel eieeuul 243 SOP 13 Protocol REVISION eien erissa rare iaa n re EAT A AEAEE EAO A AAE AA EEEE 253 Tables Page Table 1 Plant species selected for phenology monitoring in NETN designated park HANA E so vst fare Seow ae E e ra eateuca et E a a das anaaese Mediaset R 4 Table 2 Animal species selected for phenology monitoring in NETN designated park habitats iniisip ine arisia aaetoceys aaa aaaea ai a aa aidais 5 Table 3 Core and optional habitats for phenology monitoring within NETN parks Corehabitats ar shown in bold sarseiiieinnenn ia iae e ii ae Masaya aas 9 vii Executive Summary Phenology is critical to many aspects of human life and nearly all ecological relationships and processes As global climate continues to warm and change widespread shifts in phenological patterns are occurring across the globe and more change is inevitable This protocol has been developed to provide standardized methods for monitoring phenology within the National Park Service NPS Northeast Temperate Network NETN as part of the NPS Inventory and Monitoring Program I amp M NETN encompasses the Appalachian National Scenic Trail APPA Acadia National Park ACAD the Boston Harbor Islands National Recreation Area BOHA and 10 national historical parks and na
95. 8GB 11 6 12 6 17 4 23 1 25 2 34 7 69 4 138 9 16GB 23 1 25 2 34 7 46 3 50 4 69 4 138 9 277 8 32GB 46 3 50 4 69 4 92 6 100 8 138 9 277 8 555 6 64GB 92 6 100 8 138 9 185 2 201 6 277 8 555 6 1111 1 128GB 114 SOP 6 Deployment and Maintenance of Autonomous Recording Units Appendix S6 C Maintenance Log Unit Date Purchased or Produced Unit Type Circle Olympus DM 420 Song Meter SM1 Song Meter SM2 Recorder SN Mic ID R Mic ID L Additional Sensors SM2 Only Record deployment details and troubleshooting information below specifically note dates when any mics or sensors were changed for this unit as well as memory card failures Date Activity Notes T esting or trouble shooting D eployment M aintenance R emoval 115 SOP 6 Deployment and Maintenance of Autonomous Recording Units Appendix S6 D Building an External Power Cable for an SM1 or SM2 Recording Unit Materials for an external power cable reverse polarity protection and voltage regulator 6 18 gauge or thicker insulated stranded dual conductor wire 2 5 16 crimp on electrical eye terminals Conxall waterproof plug end digikey com item SC1263 ND Conxall waterproof jack digikey com item SC1272 ND 5V Switching voltage regulator dimensionengineering com item DE S W050 1A Bridge rectifier diode digikey com item 641 1211 1 N
96. A The PRA also does not apply to data collection from fewer than 10 participants Thus for this protocol the PRA would apply only to instances where 10 or more park visitors were recruited to make one time phenological observations using the same questions or data form design To comply with the PRA approval must be obtained from the Office of Management and Budget OMB prior to data collection and renewed every 3 years In August 2012 OMB granted USA NPN authorization for phenological data collection from the public Any member of the public working on NPS land or at the behest of NPS who is not a VIP is covered under this programmatic permission In addition the Privacy Act governs the collection maintenance disclosure of information from or about identifiable individuals that is maintained in systems of records by federal agencies This Act prevents the disclosure of such personal information without written consent of the 22 subject individual In order to comply with the Privacy Act data received by NETN from USA NPN does not include personal information 23 Literature Cited Blumstein D T 2009 Social effects on emergence from hibernation in yellow bellied marmots Journal of Mammalogy 90 1184 1187 Brugger R M Dobbertin and N Krauchi 2003 Phenological variation of forest trees In M D Schwartz ed Tasks for Vegetation Science 39 Phenology An Integrative Environmental Science Kluwer Academic Publishe
97. ACO two 32 GB cards and an external deep cycle battery should be able to run continuously for 21 days or for 5 minutes per hour for about 210 days 7 months without needing maintenance Make sure to load the empty memory card s with the recording schedule prior to heading into the field An SM unit running on D cell batteries will need much more frequent maintenance See the Figure S6 6 and Appendix S6 B to determine maintenance intervals for alternative recording schedules The Maintenance Log Appendix S6 C should be filled out at each visit in addition to an ARU Deployment Datasheet Appendix S6 A Upon arrival at the deployment site open the Song Meter If it is supposed to be recording during your visit you can verify that it is recording by checking the LCD screen and observing the elapsed time If you are using a daily schedule and the LCD screen is not illuminated you can press the Wake button and observe how much of the memory is full Pressing Exit will report the next scheduled event Be aware that if using an advanced schedule coded line by line on an SM1 wake sleep cycling the unit will restart the schedule at line 1 If you are not going to replace the SD card and your schedule is sensitive to sunrise sunset times or other small time shifts you should wait for the next scheduled event for 107 SOP 6 Deployment and Maintenance of Autonomous Recording Units the unit to self wake and report the card volumes An SM2 will wa
98. C NULL COMMENT Format of original survey recording WAV WAC or MP3 fldSampleRate INT NULL COMMENT Sample rate of survey recording fldBitsperSample INT NULL COMMENT Bits per sample WAV or bit rate MP3 fldChannels ENUM stereo mono NULL COMMENT Stereo or Mono PRIMARY KEY pkSurveyID CONSTRAINT fk_tblSurvey_tblCardRecorder1l FOREIGN KEY fkCardRecorderID REFERENCES acoustics tblCardRecorder pkCardRecorderID ON DELETE NO ACTION ON UPDATE NO ACTION ENGINE InnoDB COMMENT This table stores attributes of the survey recording CREATE UNIQUE INDEX pkSurveyID_UNIQUE ON acoustics tblSurvey pkSurveyID ASC koj CREATE INDEX fk_tblSurvey_tblCardRecorderl_idx ON acoustics tblSurvey fkCardRecorderID ASC Table acoustics tblArchive 197 SOP 8 Automated Sound Detection and Classification Appendix S8 B Database Schema continued DROP TABLE F acoustics IF EXISTS CR F ry F TABLE IF NOT EXISTS PRI A P HE f f kAr kSu 1dD 1dA A CONST ENGINI chiveID INT rveyID INT ateTime DA rchiveType RY KEY pkArchiveI RAINT fk_tlb NOT NULL NOT NUL iTIME NU ti y iL F E T
99. CA plug adaptor Some of the following procedure would not be needed and care will need to be taken to waterproof the connections to the RCA plug adapter Drill a 5 32 hole in the center of the plastic plate Drill 9x 1 16 holes in a ring around the center hole using the windscreen shell as a guide There is a lot of flexibility in how long the cable to the microphone could be Longer cable lengths may attenuate np fe high frequencies 4 is recommended and lengths up to 8 should ett A eA be acceptable NOTE The central hole may need to be slightly larger and then sealed with epoxy waterproof glue to accommodate feeding a PA3 microphone through the hole Cut a length of microphone cable and push 8 of it through the center hole in the plate with the short tail on the cupped side of the plate Strip 3 4 of the outer f insulation to expose the shield and twist the shield into a f pair of leads Strip back 1 2 of insulation from the R j z and L conductors but do not twist into a coherent strand N p 4 yet Insulate the back housing of the microphones with a single layer of electrical tape this will help prevent short circuits to the microphone housing Begin assembly of the first microphone by inserting the pin of the microphone into either the R or L conductor and give the strands a twist Solder the pin to the wire Solder the pin of the microphone to one of the shield leads using
100. D Perforated single sided prototype board digikey com item V2018 ND 18 gauge insulated stranded hook up wire green red and black insulation colors 1 length of 34 wide double sided mounting tape 3 4 stepped drill bit Phillips 2 screwdriver Drill Fine point craft knife Plug end Wire cutter aie a Wire stripper Solder nA als Soldering iron amp solder terminals Ohm meter volt meter Rubber Make the cable seal Strip 2 of insulation from the same end of both dual conductor wires and strip 4 of insulation from the other end Crimp the eye terminals to the ends with 2 of cable visible Slide the locking collar and rubber seal over the Locking other end of the cable solder the cable to the internal collar contacts of the plug and assemble the plug Install an external power port in an SM1 Unscrew the internal battery holder and move to the side Drill a 3 4 hole in the floor of the case of the SM1 to the left of where the battery holder sits make sure that it clears the mounting hole in the case and the battery holder Remove the internal battery holder remove the three screws visible along the lower edge in the image at right and drill a hole with the stepped bit Be sure to leave clearance for the lip of the connector and the battery holder 116 SOP 6 Deployment and Maintenance of Autonomous Recording Units Appendix S6 D Building an External Power Cable for an SM1 or
101. ETN park websites etc Contact with local native plant clubs nature centers and colleges Informational displays and flyers at visitor centers and facilities in parks and along APPA Most volunteers are trained to submit repeat observations of plant or animal phenology Participation as an observer requires a moderate every other day or at least weekly time commitment some familiarity with plant or animal identification and observation and the ability to keep careful records Training procedures for observers are provided in the NETN Phenology Observer Training Manual In addition volunteers with technical skills and interest may be trained to maintain automated recording devices and participate in processing of audio or photographic data Training for these tasks is more involved and specific and is not described in this SOP Rather training at this level occurs one on one with NPS staff or cooperators Training observers Observers that are able and willing to make repeat observations attend a 1 to 3 hour training session held annually at each participating park and within each APPA region When possible the NETN Science Communication Specialist hosts this training during annual park visits 73 SOP 3 Observer Recruitment and Training Alternatively park or regional coordinators plan and host this event each year Training focuses on understanding material in the NETN Phenology Observer Training Manual and includes A brief in
102. IMAL 8 8 NULL COMMENT Size of frequency steps 1dNTBins INT 11 NULL COMMENT Number of time bins ldFirstTBin DECIMAL 26 16 NULL COMMENT Time of first time bin in T ldNFrqBins INT 11 NULL COMMENT Number of frequency bins ldDuration DECIMAL 16 14 NULL COMMENT Duration of template seconds Fh FH FH FH A GLI E Hh Fh O C ldFrq Lim VARCHAR 45 NULL COMMENT Frequency limits of template l1dFFTwl INT 5 NULL COMMENT FFT window length Powers of 2 64 128 512 1024 2048 ldFFTovlp INT 2 NULL COMMENT FFT overlap in 1ldFFTwn VARCHAR 45 NULL COMMENT Window function name ldScoreCutoff DECIMAL 6 4 NULL COMMENT Score cutoff for template ldTemplateType ENUM BIN COR NULL COMMENT Type of template binary orrelation ldActive INYINT 1 NOT NULL COMMENT l active O inactive PRIMARY KEY pkTemplateID CONSTRAINT fk_tblTemplate_tblSpecies1l Fr fh 256 or 7 Font S E FQ PA FA Hi Mme 193 SOP 8 Automated Sound Detection and Classification Appendix S8 B Database Schema continued FORE IGN KEY fkSpeciesID REFE ON O Z H vG U zo rj Tj CREATE INDEX fk_tbl1T emplate
103. If caught in a lightning storm seek shelter in a building or car as soon as possible If no shelter is available spread out and move to an open space Squat low to the ground on the balls of your feet with your hands on your knees do NOT lie flat on the ground Avoid high elevations conductive materials and tall structures such as trees or telephone poles If you are in the open and feel your hair stand on end indicating lightning is about to strike immediately make yourself the smallest target possible and minimize contact with the ground NOTE A person struck by lightning can often be revived by prompt administration of CPR and oxygen Excessive Heat and Sun Over exposure to heat and sun can cause dehydration heat exhaustion or heat stroke All are serious conditions that can be life threatening and should be avoided When working in hot weather be sure to drink plenty of water and eat foods that can replace electrolytes Wear loose and light colored clothing including a hat to block the sun s rays It may help to shift the field schedule to avoid working outside during the hottest part of the day WARNING Signs of heat stroke include hot red or spotted usually dry skin and the sufferer may be mentally confused delirious having convulsions or unconscious If heat stroke is suspected seek immediate medical attention Poor Air Quality Summer ozone and particulate matter levels occasionally exceed federal health st
104. NE InnoDB COMMENT able to store the results of findPeaks CREATE INDEX fk_tblSpeciesResults_tblTemplatesl_idx ON acoustics tblResult fkTemplateID ASC CREATE INDEX fk_tblResults_tblSurveyl_idx gt ON acoustics tblResult fkSurveyID ASC 199 Person who performed automated detection Peak correlation t his species z SOP 8 Automated Sound Detection and Classification Appendix S8 B Database Schema continued CREATE INDEX fk_tblResults_tblPersonl_idx ON acoustics tblResult fkPersonID ASC Table acoustics tblPersonContact DROP TABLE IF EXISTS acoustics tblPersonContact CREATE TABLE IF NOT EXISTS acoustics tblPersonContact fkPersonID INT NOT NULL COMMENT This field is a foreign key that is linked to tblPerson and references a person s PKPersonID fldContactInfo VARCHAR 45 NOT NULL COMMENT The value is the contact value itself e g 802 123 4567 or johndoe gmail com fldcontactType ENUM Work Phone Cell Phone Email NULL COMMENT The contact type is restricted to an enumerated list Options listed include Work Phone Cell Phone and Email those this can be expanded if desired PRIMARY KEY fkPersonID fldContactInfo CONSTRAIN
105. NT Store the names of multiple projects per organization here CREATE UNIQUE INDEX pkProgramID_UNIQUE ON acoustics tbProject pkProjectID ASC CREATE INDEX fk_tbProject_tblOrganizationl_idx ON acoustics tbProject fkOrganizationID ASC 195 SOP 8 Automated Sound Detection and Classification Appendix S8 B Database Schema continued Table acoustics tblCardRecorder DROP TABLE IF EXISTS acoustics tblCardRecorder CREATE TABLE IF NOT EXISTS acoustics tblCardRecorder pkCardRecorderID INT NOT NULL AUTO_INCREMENT fkPersonID INT NULL COMMENT The person who deploys the recording unit i fkRecorderID INT NOT NULL COMMENT This foreign key references the unit number pkUnitID stored in tblRecordingUnits fkLocationID INT NOT NULL COMMENT The location in which the unit was deployed fkCardID INT NOT NULL COMMENT This is a foreign key referencing the pkCardID in tblCard fkProjectID INT NULL fldDateDeployed DATETIME NULL COMMENT The date that the card was
106. NWauto 8 8 953 92 442 2 098 2 773 4950 0 4 BTNWauto 2 8 906 83 995 ZOR OIA Ze hoe 2200 0 4 Score information min score max score n scores BTNWd1 0 0429 0 79 28340 BTINWpartial 0 16 0 81 28338 BINwd 8 0432 0 78 28337 BTNWd 5 0 31 0 79 28339 BTNWd 2 0 34 0 79 28339 BTINWauto 8 0 15 0 65 28329 BTNWauto 2 0 16 0 65 28330 The next step is to identify events within the score list using the cutoff threshold stored in the template This is done with the findPeaks function Binary Point Matching In some cases Binary Point Matching may be a better method than Spectrogram Cross Correlation First load the templates into the R workspace The function to do this will vary depending on where your templates are stored The function binaryPtMatch performs the point match detection and classification By default it uses a window length of 512 with an overlap of 0 If using Linux or MacOS you can set parallel TRUE for faster processing Speed should increase linearly with an increase in the number of cpu cores Detection of some calls may be improved by changing the FFT window length FFT overlap or FFT window function If you need to do this the binaryPtMatch function will pass the argument to spectro gt scores lt binaryPtMatch survey C Users jkatz3 Dropbox LabDemo Surveys MABI2_A_062510 wav template L BINtemplates parallel FALSE gt scores A templateScores object Survey information Wave Object N
107. National Park Service j is U S Department of the Interior Natural Resource Stewardship and Science k Phenology Monitoring Protocol Northeast Temperate Network Natural Resource Report NPS NETN NRR 2013 681 ON THE COVER Clockwise from top left close up of rough stemmed goldenrod with fruits unripe goldenrod with fruits ripe red maple leaf in fall color at Marsh Billings Rockefeller NHP and Audio Recording Unit being set up in March at Marsh Billings Rockefeller NHP by SCA intern Amanda Anderson Photographs by Top Boston Harbor Islands National Recreation Area bottom Ed Sharron Phenology Monitoring Protocol Northeast Temperate Network Natural Resource Report NPS NETN NRR 2013 681 Geri Tierney Brian Mitchell Abe Miller Rushing Jonathan Katz Ellen Denny Corinne Brauer Therese Donovan Andrew D Richardson Michael Toomey Adam Kozlowski Jake Weltzin Kathy Gerst Ed Sharron Oliver Sonnentag Fred Dieffenbach Department of Environmental amp Forest Biology SUNY College of Environmental Science amp Forestry Syracuse NY 13210 Northeast Temperate Network 54 Elm Street Woodstock VT 05091 gt Acadia National Park Schoodic Education and Research Center Bar Harbor ME 04609 Vermont Cooperative Fish and Wildlife Research Unit Rubenstein School of Environment and Natural Resources The University of Vermont Burlington VT 05405 National Coordinating Offi
108. Richardson Michael Toomey Geri Tierney Position USA NPN Monitoring Design amp Data Coordinator USA NPN Assistant Director Contact for Partner Datasets Collaborator on acoustic methods University of Vermont Collaborator on automated camera methods Harvard University Collaborator on automated camera methods Harvard University Collaborator SUNY ESF Email ellen usanpn org alyssarosemartin gmail com tdonovan uvm edu arichardson oeb harvard edu mtoomey fas harvard edu gtierney esf edu 35 SOP 1 Safety Northeast Temperate Network Version 1 00 Overview The Northeast Temperate Network NETN considers the occupational health and safety of its employees cooperators contractors and volunteers monitoring staff to be of utmost importance and is committed to ensuring that all personnel receive adequate training on National Park Service NPS safety procedures incident reporting and emergency response prior to field work This SOP and supporting appendices were designed to provide a summary of safety issues that should be reviewed and understood by anyone participating in the phenology monitoring protocol and to serve as a first reference in case of an incident Topics covered include emergency procedures and contacts incident reporting field preparation safe field procedures vehicle safety and workers compensation procedures A Green Amber Red Risk Assessment GAR has been conducted for this pr
109. SM2 Recording Unit continued Add reverse polarity protection to an SM1 or SM2 Cut a section of the perforated circuit board so that you have at least a 2x4 hole pattern to work on Cut two pieces of green hookup wire 3 long and strip 1 8 of insulation from all ends Solder one end of each wire side by side in adjacent holes at one end of the perforated board Cut a 4 length of red hookup wire a 4 length of black hookup wire and a 3 length of black hookup wire At the opposite end of the perforated board enlarge the hole that will correspond to the negative output from the rectifier diode this should be marked on the top of the diode the hole should be large enough to fit two wires through Pass the end of the black 4 and 3 section of wire through and solder to the board Solder the red 4 piece through the board next to it The board should now have two green wires at one end and a red wire and a black wire at the other end and the two ends should be separated by a 2x2 square of holes Place the bridge rectifier on top of the soldered wires so that the 4 pins mate up with the 4 wires with no potential to short circuit Be sure that the two pins marked line up with the green wires the positive pin lines up with the red wire and the negative pin lines up with the black wire Solder the pins to the wires Solder a green wire to each pin of the external power port If working on an SM2 you will need to first
110. Sample rates 4 8 16 22 05 24 32 44 01 and 48kHz standard 192kHz and 384kHz available with SM2BAT192x2 and SM2BAT384 dauther cards e Digital format 16 bit PCB wav or proprietary lossless and lossy compression formats wac e Headphones 3 5mm stereo jack e Filtering and triggering Configurable digital high pass and low pass filters at sample rate divided by 3 4 6 8 12 16 24 32 48 and 96 Adaptable trigger with configurable threshold above background 1 88dB absolute trigger with configurable threshold 1 88dB full scale inactivity time for trigger off 0 1 9 9 seconds Sensors e Channels 2 e ADC 10 bit at 3 3V reference 3 2millivolt resolution e Parameters available for precise calibration e Internal temperature sensor accurate to within 2 C at 0 C e External sensor port with 3 pin waterproof connector ground signal 3 3V supply Storage e 4 SD SDHC SDIO flash card slots Class 4 or greater e 128GB total capacity with 4x32GB cards available today more as higher capacity cards become available e Compression increases effective capacity by 60 70 typically Power e 4 10VDC main power internal 4 D size batteries or external weatherproof connector e 6 20VDC through external power adapter for 6 or 12V solar power systems e lt ImA when idle between scheduled recordings e The following estimates can vary 10mA depending on flash cards used e 55 65mA when recording uncompressed up to 48kHz exc
111. T fk_tblPersonContact_tblPersonl FOREIGN KEY fkPersonID REFERENCES acoustics tblPerson pkPersonID ON DELETE NO ACTION ON UPDATE NO ACTION ENGINE InnoDB COMMENT Contact info including Cell Work Phone and email Use xxx comment truncated Table acoustics tblEvironmentalData DROP TABLE IF EXISTS acoustics tblEvironmentalData CREATE TABLE IF NOT EXISTS acoustics tblEvironmentalData pkEnvironmentalData INT NOT NULL fldType ENUM WindSpd AirTemp SkyCode AtmosPress NULL tblCardRecorder_pkCardRecorderID INT NOT NULL PRIMARY KEY pkEnvironmentalData CONSTRAINT fk_tblEvironmentalData_tblCardRecorderl FOREIGN KEY tblCardRecorder_pkCardRecorderID REFERENCES acoustics tblCardRecorder pkCardRecorderID ON DELETE NO ACTION ON UPDATE NO ACTION ENGINE InnoDB CREATE INDEX fk_tblEvironmentalData_tblCardRecorderl_idx ON acoustics tblEvironmentalData tblCardRecorder_pkCardRecorderID ASC SET SQL_MODE OLD_SQL_MODE FOREIGN_KEY_CHECKS OLD_FOREIGN_KEY_CHECKS SET UNIQUE_CHECKS OLD_UNIQUE_CHECKS n 200 SOP 8 Automated Sound Detection and Classification
112. V file with all clips of a species within it which you should assign to an object hits btnw lt collapseClips rec survey start times BINdetectionsStime 1 5 end times BINdetectionsStime 1 5 The output is a single wave object containing all hits bound together which you could write to a wave file writeWave hits btnw E users jkatz3 ArchivedHits Surveyl btnw wav If you write the object to anew WAV file for archiving it will be useful to make a key to identify when in the original survey each clip occurred To record this add the return times argument to collapseClips hits btnw lt collapseClips rec survey start times BINdetectionsStime 1 5 end times BINdetectionsStime 1 5 return times TRUE The output will now be converted to a list in which the first element is the wave object and the second element is a data frame of the start and end time for each clip gt names hits btnw 1 wave times You can write the wav object to a file using an almost identical call but specifying the item in the list writeWave hits btnw wave E users jkatz3 ArchivedHits Surveyl btnw wav You can then attach the key to the list of detections from findPeaks BINdetections lt cbind BINdetections key times hits btnwStimes The list of detections could then be saved as a comma separated values csv file and archived with the sound clips The sole disadvantage of archiving events is the volume of
113. YY MM DD HHMMSS TZX wac A csv will be produced containing all of the new wac file names and original dates modified and it will be saved in the directory specified in the command The name of the csv file will default to the location prefix followed by the time the files were copied but you can use the argument csv name to specify a custom name if you prefer In the csv the date modified on the wac files matches the original of the files still on the card but the files will display a new date created these are copies of the original files but not the original files Although they are newly created no samples have been added or removed from the data portion of the file The survey names in the csv will not match the actual file names exactly Kaleidoscope will change the file name during file conversion so the survey name in the csv will match the file name after conversion to wav format 162 SOP 8 Automated Sound Detection and Classification Specifying a CardRecorderID from tblCardRecorder pkCardRecorderID completes the link that joins each survey file to both the recorder that recorded it and the card it was recorded to Failure to specify this value will not cause the database to reject the metadata upload but it will prevent the user from making queries that rely on that connection in the future If using a database the next step is to upload this metadata to the database to keep it safe Refer to that section in the upload to
114. a National Historical Park USA NPN USA National Phenology Network xiii USGS United States Geological Survey WEFA Weir Farm National Historic Site xiv Background and Objectives Phenology is the study of the timing of recurrent biological events the causes of their timing with regard to biotic and abiotic forces and the interrelation among phases of the same or different species Lieth 1974 Phenological events include the beginning and end of flowering leaf out migrations hibernation and other similar seasonal biological events Phenology is critical to many aspects of human life e g agriculture gardening health cultural events and recreation and nearly all ecological relationships and processes e g plant pollinator and predator prey relationships competition and carbon and water cycling Schwartz 2003 This protocol has been developed for monitoring phenology within the National Park Service NPS Northeast Temperate Network NETN including the Appalachian National Scenic Trail APPA as part of the NPS Inventory and Monitoring Program I amp M NETN is one of 32 ecoregional networks established by NPS to facilitate expanded inventory and monitoring activities These networks monitor Vital Signs which are a subset of physical chemical and biological elements and processes of park ecosystems that are selected to represent the overall health or condition of park resources known or hypothesiz
115. a a a A E A one Oe ix PLC KATOW IES TTC M Shc sess scat aoe n a n E T E A a a a a tcc cn tie xiii Listof Terms atid A cron yinis sai oer an dsta et auneaie te he aes a a a aaai xiii Background arid ObjettiyESssiieni inei niece RE E en linea 1 USS ELE AHO I ae aaa aa aed ac lad al Ra Saal Pa Na end Nl Pah oan ak a BN 1 Existing Protams ars esis ncnszeracesbansazessaanhacpheton darian PE NEES EAA EE EEEO AAAS A ETE AAE SENA ERES aS 2 Pilot Project neesiet e O E E T T E O E 2 Goals and Objectiyes notia a E e AEE AEAT EE A ERAR 3 Sampling ES FO Tia cs cent coauict culpa com EEE E E A E tacetanees 7 PISO AG hy waa Tau these vated Rank a en tend age tctitl ectau Se ticeny dentate 7 Sampling Frame and Site Sel Ct OM 0ss lt caxciivcadsercdtvasts eagisadoGl oaaeeaas MiesnioG avaaniastsavhtea ees 8 Frequency and Rephcation cdet acess a meade cae Auden ok Gane aaa 10 Species and Individual Selection xcsicyttccisei ein esivat ced ela ee satencea eae 10 Detectable Revel ore Nantes wens ost ai tales eects gh nach a e occa Santee jos 11 WASTES EE E A E E EE 13 Field Season Preparations sesiewsoactisehsuaus a ptk ai a E A E E 13 Establishing Sitesini aea e a cote Sats a a a a e eaaa 13 Sequence of Events During the Field Season ccsecccssccsescssrceseccsseccssccescestaceesasesenenses 14 Makino OBSet vations cscs ce nas haa cise anise urnan iE de em austen ound aero ied 14 Automated Data senikto norinni a a Faden Madan aeven ae aiaa 14 Data Pro
116. a to the database only once using the dbUploadSurvey function and setting the argument update FALSE View the arguments for this function using the args command gt args dbUploadSurvey function db name acoustics uid default pwd default surveys update query FALSE The allow the user to add additional arguments to odbcConnect If you have set up your ODBC connector to save your database username and password the initial call will look like this dbUploadSurvey db name acoustics surveys surveydata If you opt to enter that information at each use you can specify that information in the call dbUploadSurvey db name acoustics uid dbuser pwd sEcurePaSsl1 surveys surveydata A successful upload will return the time taken to run the insert query and an unsuccessful upload will return the error message provided by the MySQL server Read Saved Templates Read correlation templates from the local disk Use the function readCorTemplates to read one or several templates Specify which templates to read in the directory in which they reside and the name of the object they will be assigned to CORtemplates lt readCorTemplates files c BTNW_rect_C BTNW_rect_C NW_rect_d50_C BTNW_rect_d50_C NW_auto_d80_C BTNW_auto_d80_C NW_line_d100_C BTNW_line_d100_C NW_click_allNotes_C BTNW_click_allNotes_C dir C Users jkatz3 Dropbox LabDemo Templates 2i Be 4 B
117. abDemo Templates BINW wav 129 SOP 7 Acoustic Template Creation select click 140 Frequency kHz N Frequency kHz m 80 Time s Time s Frequency kHz 0 5 1 1 5 2 2 5 Time s Figure S7 4 Top left call 9 line selection at density 1 0 Top right line selection call 10 at density 0 5 Bottom point click selection Combine templates for uninterrupted analysis adjust score cutoff rename them Templates can be used for spectrogram cross correlation as soon as they are made but to scan a survey with multiple templates you must combine them into a list It is possible to combine templates with multiple FFT parameters into a list but the FFT will need to be recomputed for each template which will add several seconds to each pass Combining the templates will also expedite saving them for future use either locally or in a database The combineCorTemplates function is demonstrated below This call assigns a default score cutoff for all templates CORtemplates lt combineCorTemplates BTNW_rect_C BTNW_rect_MandHnotes_C BTNW_rect_qd80_C BTNW_rect_d50_C BTNW_rect_d20_C BTNW_auto_d100_C 130 SOP 7 Acoustic Template Creation BTNW_auto_d80_C BTNW_auto_d20_C BINW_line_d100_C BTNWlineO 5_C Miss one Add templates to that list as well CoRtemplates lt combineCorTemplates CORtemplates BINW_click_allNotes_C This call re
118. able NETN to consider volunteer skill level while complying with the Privacy Act Automated analysis will identify phenology outliers greater or equal to one month from expected dates based on the accumulated dataset Outliers of this magnitude are typically recording errors these outliers will be excluded from trend analysis Data Stewardship Subsampled audio files from Song Meter recorders and Olympus ARUs are stored by participating parks using duplicate external hard drives Each Song Meter ARU operating as recommended subsample 10 minutes per hour and convert to WAV file generates about 1 0 Gb per day of raw audio data Each Olympus ARU subsampled as recommended in the Automated Sound Detection and Classification SOP subsample 10 minutes per hour as MP3 generates about 0 4 Gb per day of raw audio data Note that only the subsampled raw data are processed and stored the remainder of the data stream is discarded 224 SOP 11 Data Management and Quality Assurance Quality Control Each webcam operating as recommended 1 MB jpg photo captured every 2 hour for 14 hours day generates about 28 MB per day of raw image data Each plant cam operating as recommended 1 MB jpg photo captured hourly for 10 hours day generates about 10 MB per day of raw image data Image files from automatic cameras are stored by participating parks on external hard drives and also on the PhenoCam server as described below On the PhenoCam server image data
119. able that monitoring staff learn to recognize this plant and take precautions to avoid skin contact with any part of it Using a pre exposure cream and wearing long sleeves and long pants can help reduce the amount of skin contact with the plant If needed use poison ivy wipes after contact Monitoring staff should be careful not to rub their faces when working around poison ivy After working in an area with abundant poison ivy monitoring staff should gently wash exposed skin in cool water with poison ivy soap and should change into fresh field clothes At the end of a field day monitoring staff should also wash potentially contaminated equipment e g backpack If a severe allergic reaction occurs the affected individual should seek medical attention notify the park Natural Resource Manager as soon as possible and file a workers compensation claim Venomous Snakes The following species of venomous snakes may occur in some NETN parks copperhead Agkistrodon contortrix cottonmouth Agkistrodon piscivorus and timber rattlesnake Crotalus horridus The best course of action is to avoid all snakes by keeping them at a safe distance When in poisonous snake country pay attention to where you put your hands and feet and be aware around rock piles and bedrock outcrops Note that many snake bites are purely defensive and contain no venom Bites from immature snakes are much more likely to contain a more dangerous amount of venom than bites from
120. above the specified threshold as on points and all those below the threshold as off points This option is enabled by changing the select argument to auto as in the following command Call 3 two Song Sparrow clips using click selection SOSP_auto_d50_b4_midphrase_B lt makeBinTemplate2 clip L list s6 home jkatz3 Dropbox UVMacoustic Analysis bird Recordings s6 wav s7 home jkatz3 Dropbox UVMacoustic Analysis bird Recordings s7 wav t lim L list c 1 4 4 5 c 1 4 1 frq lim c 2 8 select auto amp cutoff 31 dens 0 5 buffer 4 name SOSP_auto_d50_b4_midphrase_B After setting the amplitude cutoff and time shift the automatic point selection takes place 145 Frequency kHz SOP 7 Acoustic Template Creation 50 100 150 200 250 300 90 E EE i ro E rt a if 6 end chills tt 70 s fitted ee th 60 u MOE ee Abe khh N I LLLI 1 50 4 sits ee ARNIS 3 AIALL L ee oe 7 30 0 5 1 1 5 2 2 5 3 3 5 Time s Figure S7 16 Call 3 Automatic selection at a reduced density and with a 4 point buffer Combine templates for uninterrupted analysis adjust score cutoff rename them Templates can be used for binary point matching as soon as they are made but to scan a survey with multiple templates you must combine them into a list It is possible to combine templates with multiple FFT parameters into a list but the FFT will need to be recomputed for each template which will add se
121. aff must rename Olympus files using the procedure outlined in the Automatic Sound Detection and Classification SOP or Bulk Rename Utility software see Appendix S11 A Note that for Olympus datafiles it is necessary to adjust the filename to properly reflect the START of data capture not the time the file was created This adjustment is made during file renaming by subtracting the audio file length from the file s modified date using an offset command as shown in Appendix 11 A Song Meters automatically name files using the START time of data collection so no adjustment is necessary for Song Meter files Raw audio files from Olympus mp3 and Song Meter wac converted to wav ARUs PARK HH YYYYMMDD HHMMSS Where PARK the four letter NPS acronym corresponding to the park of deployment e g ACAD HHHH the four digit site number assigned by USA NPN for the site of deployment YYYY MMDDHHMMSS the START date time of data capture year month day hour minute and second Uploading to PhenoCam Server Coordinators at parks collecting images upload images to the PhenoCam server as soon as possible after collection using the instructions provided in Appendix C Legislative Requirements To comply with the Privacy Act data received by NETN from USA NPN does not include personal information Observers are indentified by an identification number assigned by USA NPN Literature Cited USA NPN Technical Information Sheet Data Qu
122. ality Assurance amp Quality Control for Nature s Notebook Ver 1 0 October 2011 www usanpn org files shared files USA NPN_QA QC tech _info_sheet_3 2012 pdf 226 Revision History SOP 11 Data Management and Quality Assurance Quality Control Version Date Revised by Changes Justification 1 00 Sept 2010 Geri Tierney Adapted from the NETN Forest Protocol Data Management and QA QC SOP version 2 1 Includes Privacy Act Requirements 1 01 Nov 2010 Geri Tierney Clarification of legal requirements and data Adam storage Editorial changes Kozlowski 1 02 April 2011 Brian Mitchell Clarified this SOP is for Observer data only Geri Tierney Eliminated custom sites Clarified that data from one time observers must also be stored in NPN database Editorial changes 1 03 March Geri Tierney Removed park logbook instructions 2012 1 10 Jan 2013 Geri Tierney Added data stewardship for automated Adam recorder data Added instructions for Bulk Kozlowski Rename Utility Expanded QA QC discussion Revised to include observations by untrained observers Revised discussion of Privacy Act compliance Added flow chart of responsibility Noted that SongMeter files are subsampled Added Appendix C for uploading to PhenoCam server 1 11 Jan 2013 Ellen Denny Edited references to USA NPN Editorial Geri Tierney changes Updated Appendix C Brian Mitchell 1 12 May 2013 Geri Tierney Editorial changes Adjusted file renaming Resp
123. als and Objectives The overall goal of NETN phenology monitoring is to determine the trend in phenology of key species in order to assist park managers with the detection and mitigation of the effects of climate change on park resources An additional programmatic goal is to interest and educate park visitors and staff as well as a cadre of volunteer monitors Specific monitoring objectives of this protocol are to e Develop and maintain a list of key species that are of scientific or management interest and are suitable for phenology monitoring within NETN parks To be suitable a species must be readily identifiable by trained observers or by automated acoustic or photographic techniques and exhibit observable phenophases In addition preference is given to species with legacy data sets available for comparison e Detect long term trends in timing and abundance of monitored phenophases of key species at index sites in designated core and optional park habitats e Explore correlations between phenological data and climate variables including mean monthly temperature and degree days in order to develop hypotheses about impacts of climate change on phenology We focus network wide efforts on a short list of selected species in order to provide sufficient data to determine trends Fifteen plant and twelve animal species occurring within two core habitats Northern hardwood forest and Vernal pools and five optional park habitats have been selec
124. am Wide HD 40 1920 1 3 0 1 3 0 2 StarDot NetCam Regular 37 1300 15 1 60 5 StarDot NetCam Wide 94 1300 25 3 100 13 206 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras For monitoring greenness of a vegetation canopy the camera is mounted at a location offering a vantage of the canopy such as an overlook or a tower The field of view must show more canopy than sky an ideal ratio is 80 canopy and 20 sky Adjust zoom if necessary to achieve this balance If possible camera should be mounted 5 10 m above the canopy and looking slightly downward at approximately 10 20 Also cameras should be mounted pointing north to minimize light interference from the sun and ree yp Figure S9 1 Ideal field of view for forward scatter It is important that the area within monitoring a canopy at Harvard Forest the camera s field of view that automatically adjusts exposure be aimed at the canopy not at the sky Figure S9 1 shows an ideal field of view for monitoring a canopy at Harvard Forest Install webcams within weatherproof housing as directed by instructions for your specific model Remember to remove the camera s lens cap before installing the camera Slide the camera forward in its housing so the lens is almost touching the window to minimize the potential for reflections and glare Plant cams and webcams are mounted firmly to minimize shifts in field of view Wingscapes plant cams have two
125. and request a corresponding list from USA NPN showing the corresponding observer id numbers within each class During regression analysis any outlier event dates with residuals estimated to be greater than or equal to 30 days are considered month mistakes and excluded from data analysis Schaber et al 2010 Additional data points that look unusual may be flagged during data analysis for verification Descriptive statistics For selected phenophases of each monitored species see Appendix 12 A calculate annual mean and standard deviation of event dates from all individual plants and from all animal sites For each species plot the mean event date and SD across years showing event date on the Y axis expressed as day of year for a non leap year and year on the X axis For select phenophases of monitored species illustrate phenophase distribution by plotting the 1 proportion of monitored individuals exhibiting selected phenophases through the current year and or 2 the recorded abundance of phenophase events through the current year Show proportion of individuals or abundance classes on the Y axis and event date on the X axis expressed as day of year for a non leap year For each event date of an individual plant or an animal species at a site calculate the difference in days between the mean event date from the multi year dataset and the current year s observation For selected phenophases of monitored species plot the differ
126. andards Young children seniors and those suffering from asthma chronic bronchitis and chronic obstructive pulmonary disease or heart problems are especially sensitive to poor air quality and should minimize outdoor activity when poor air quality warnings are posted The risks of occasional exposure to ozone and fine particulate matter are minimal for healthy individuals 41 SOP 1 Safety When poor air quality warnings occur it is advisable for monitoring staff to avoid overly strenuous activity during the hottest part of the day pollution levels tend to be lowest early in the morning and to stick to lower elevations under a forest canopy To check local air quality forecasts or learn more about health risks of air pollution visit the AIRNow intergovernmental agency website http www airnow gov Deer ticks and Lyme Disease Several species of ticks are commonly encountered in eastern U S parks while working in the field Figure S1 1 This includes the deer tick Ixodes scapularis which is a known vector of Lyme disease and Ehrlichiosis Infected deer ticks are abundant from New Jersey to southern New Hampshire and common elsewhere in New England and Lyme disease is a serious Safety concern in all NETN parks Monitoring staff must take the precautions outlined below to help minimize the chances of having an embedded tick that could lead to illness e Clothes treated with tick and insect repellents have been found to
127. anipulation in black Core analysis in red Wey MO eon jeuy a 8S xipueddy SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras Northeast Temperate Network Version 1 10 Overview Digital timelapse photography can be an important data source for long term phenological research providing a consistent and objective stream of data at optimal frequency in both accessible and remote locations This SOP describes procedures for selecting deploying and maintaining automated digital cameras for long term phenological observation of individual plants and vegetation canopies Selecting a digital camera Comparison of a variety of camera types of varying price and quality showed little difference in ability to detect phenological trends among image datasets collected using inexpensive outdoor webcams cameras directly addressable via Internet Protocol and game and plant cameras basic time lapse cameras targeted at hobbyists for outdoor use herein called plant cams and images taken by more expensive webcams and digital single lens reflex cameras Sonnentag et al 2012 For this protocol NETN uses both outdoor webcams and plant cams The choice between an outdoor webcam or a plant cam for a specific site is made by park personnel considering the availability of site infrastructure user skills and to some extent cost Webcams require an external power supply and computer network infrastructure at the monitoring s
128. arch Geri Tierney Removed text describing casual observer 2012 methods Add instruction for registering site at USA NPN and designating multi observer site Added section for registering plants including patch monitoring Editorial changes 1 2 Nov 2012 Geri Tierney Removed metadata field description and replaced with reference to USA NPN methods and technical information sheet Added USA NPN recommended Nature s Notebook text Added guidance to park managers on species selection and walking route Editorial changes 1 21 Nov 2012 Geri Tierney Added patch monitoring instructions Added datasheets for collection of site data and plant registration information Added site naming guidelines Reinserted informational displays to attract one time or initial observers at public sites 1 22 Jan 2013 Ellen Denny Edited references to USA NPN Clarified Geri Tierney monitoring frequency Added patch size to datasheet Editorial changes 1 23 March Geri Tierney Reformatted plant registration datasheet to 2013 accept 3 plants per sheet 70 Appendix S2 A Datasheets NETN Phenology Site Datasheet Version 1 00 These USA NPN data fields are recorded when sites are setup for monitoring and entered online into USA NPN s National Phenology Database via Nature s Notebook Update annually or if conditions change Station code or site name Date recorded Latitude Longitude of Record at the center of the site in decima
129. ary key for ldFirstName 1dMiddleName VARCHAR 45 VARCHAR 45 VARCHAR 45 pkPersonID acous NOT N NULL NOT NULL tblPerson r tics tblPerson INCREMENT COMMENT tically assigned to the table iL COMMENT The COMMENT The COMMEN The U individuals Names of people in the monitoring program Tab le acoustics tblLocation DROP T F ABLE IF EXISTS CR EFA ry F TABLE Li pki d ocationl socationNn ati d loc on Fore ocationNn abb atitude Map r Google IF NO D Earth EXISTS INT ame VARCHAR 100 xample ameAbbreviation reviation for the location name NT DOUBLE NULL COMME can be used Map Mh WM MAU MA d O ld O ld EN d COMM r Google ongitude Earth can be used sE DOUBLE NULL COM acoustics acous NOT NULL AUTO_ automatically assigned and serve as the N Saratoga Na ENT tbhlLocation Thes tbhlLocation ENT COMMENT ELES ao INCREM numbers individuals first name individuals middle name last name ECKS 0 D_DATES The unique ID assigned to ach person and the ig r a the primary ENT The Historic Park NOT NULL COMMENT SARA01 Required
130. at actually will hold your data Choose the location nearest you and press Next 184 SOP 8 Automated Sound Detection and Classification Appendix S8 A Creating a MySQL database continued New DB Instance x Step 2 of 3 Product Xeround BASIC Please select the Data Center where you want to run your database Data Center Rackspace US ORD1 Chicago Amazon EC2 US East Virginia Amazon EC2 EU West Ireland Rackspace UK LON3 London gt Cancel lt Previous seattle Then fill out the form that follows Here you ll enter the name of your database Acoustics and identify a username and password Jot these down because you ll need to use them to connect the database with R 185 SOP 8 Automated Sound Detection and Classification Appendix S8 A Creating a MySQL database continued New DB Instance Step 3 of 3 Product Xeround BASIC Data Center Amazon EC2 US East Virginia Plan Trial Please fill in the following details DB Instance Name User Name Password Re type Password DB Instance Description Cancel Acoustics username eeeeoooo A This database stores acoustic monitoring data a oe Press Create and you should see the name of your database listed in the DB Instance Manager Click on database name then look at the database details in the lower panel I Acoustics Acoustic Monitoring 2 Instance ID 29243 v3 2 1 112 Plan Xeround FREE
131. ated audio recording can be an important data source for long term phenological research providing a consistent and objective stream of data at optimal frequency in both accessible and remote locations This SOP provides specific procedures for the deployment and maintenance of a homemade autonomous recording unit ARU that contains an Olympus digital recorder and the Song Meter recording unit by Wildlife Acoustics Inc The Wildlife Acoustics SM1 units depicted in this SOP are no longer available they have been replaced by the SM2 Deployment of Olympus and Song Meter ARUs requires slightly different procedures which are described in separate sections of this SOP The process for downloading and storing audio data collected by these units is also covered by this SOP This procedure was developed by Corinne Brauer and Jon Katz of the Vermont Cooperative Fish and Wildlife Research Unit at the University of Vermont The decision regarding which type of ARU to deploy is up to the individual park The Song Meters are more convenient more powerful and come with a certain amount of technical support but they also have a higher price tag about 800 for the unit batteries and memory cards Do it yourself ARUs are significantly cheaper and offer a potential learning experience e g for a high school science class for about a quarter the price 93 SOP 6 Deployment and Maintenance of Autonomous Recording Units Deployment of Olympus ARU
132. ated individual Conduct field work Check in with RM DI after field work to remote or hard to access site DO NOT FORGET 62 SOP 1 Safety Appendix S1 C Safety Forms continued Phenology Monitoring Trip Plan for Remote or Hard to Access Sites This form must be completed and e mailed to the park resource manager or other designated individual in advance of your monitoring trip to a remote or hard to access site If you are monitoring a route at Acadia and will be borrowing the NETN SPOT GPS Messenger and Personal Locator Beacon NETN staff will need a copy of this trip plan and contact information for the individual who will be serving as your official check in Name of monitor Cell phone number Home phone number Name of monitoring partner Partner cell phone number Partner home phone number Date of trip Start time End time Check in time Warning if you do not check in by this time an attempt will be made to reach you by phone if you do not respond emergency services will be notified Do not forget to check in Vehicle make model and license plate Planned parking location s Route to be monitored Note the person receiving this trip plan must have a map of the route 63 SOP 1 Safety Revision History Version numbers will be incremented by a whole number e g Version 1 30 to 2 00 when a change is made that significantly affects requirements or procedures Version numbers will be
133. ates function gt args dbUploadTemplates function template L which one NA db name acoustics uid default pwd default analyst locationID date recorded recording equip species code The which one argument allows upload of just a single template in the list rather than the whole list Leave the default NA to send the whole list The allows additional arguments to be passed to odbcConnect This function requires that the connection to the database be established in your ODBC manager if you do not have a database username and password stored in your ODBC manager you may use the uid and pwd arguments to supply them here The analyst and locationID arguments require the key values from tblPeople pkPersonID and tblLocation pkLocationID The optional recording equipment argument allows you to name the type of recorder used and the required species code allows you to specify a species code from tblSpecies fldSpeciesCode For birds this is the standard four character BBL codes but for other species it may be four six or eight character codes derived from the latin nomenclature In all cases the codes must exist in tblSpecies prior to assigning them to a template This call demonstrates how to create a vector of species codes but in this case one code could have been used and it would be recycled dbUploadTemplates templates CORtemplates analyst 2 locationID 9 recording equip Sennheisers
134. ates s21l wav s22 E users jkatz3 Desktop SOSPtemplates s22 wav s23 E users jkatz3 Desktop SOSPtemplates s23 wav frq lim L list default c 1 55 8 96 score cutoff L list default 0 3 Bind all of these clips together into a single file and separate each clip by at least 1 second of noise Add a bit of noise by finding 1 2 seconds of noise highlighting it in Audacity and exporting the selection to the SOSPtemplates folder Then read it into R noise lt readWave file E users jkatz3 Desktop SOSPtemplates noise wav sl lt readWave E users jkatz3 Desktop SOSPtemplates sl wav s2 lt readWave E users jkatz3 Desktop SOSPtemplates s2 wav 149 SOP 7 Acoustic Template Creation s3 lt readWave E users jkatz3 Desktop SOSPtemplates s3 wav s4 lt readWave E users jkatz3 Desktop SOSPtemplates s4 wav s5 lt readWave E users jkatz3 Desktop SOSPtemplates s5 wav s6 lt readWave E users jkatz3 Desktop SOSPtemplates s6 wav s7 lt readWave E users jkatz3 Desktop SOSPtemplates s7 wav s8 lt readWave E users jkatz3 Desktop SOSPtemplates s8 wav s9 lt readWave E users jkatz3 Desktop SOSPtemplates s9 wav s10 lt readWave E users jkatz3 Desktop SOSPtemplates s10 wav s11 lt readWave E users jkatz3 Desktop SOSPtemplates sll wav s12 lt readWave E users jkatz3 Desktop SOSPtemplates s12 wav s13 lt readWave
135. b name acoustics by type ct FFTwl 512 FFTovlp 50 To download specific templates by name specify them by entering a vector of names in the template group argument and setting the by cat argument to names Download just a few correlation templates specifying them by template name CORtemplates lt dbDownloadTemplates db name acoustics by type ct FFTwl 1024 FFTovlp 50 by cat names template group c BTNW_d05_Buff3_ovlp50_w11024_BIN Or to download all templates for a particular species specify them by entering a vector of species codes in the template group argument and setting the by cat argument to species Download just a few correlation templates specifying them by species code CORtemplates lt odbcDownloadTemplates by type ct FFTwl 1024 FFTovlp 50 by cat species template group c BINW SOSP The resulting object is a template list ready to be used in the appropriate analysis either spectrogram cross correlation or binary point matching 166 SOP 8 Automated Sound Detection and Classification View previously constructed templates View the templates in a template list simply by using the plot method for template lists After entering the plot yourtemplate command pressing return will advance to the next template in the list The example below uses this function to illustrate how the buffer argument can be used to effectively separat
136. be 0 33 indicating a grey that is an equal mix of red green and blue throughout the year and should not show obvious seasonality Digital camera settings Most configuration settings are kept on default or automatic settings One exception is that white balance sometimes referred to as color balance is set manually to the fixed setting sometimes referred to as manual or outdoor settings for webcams if possible in order to minimize in camera processing of day to day changes in illumination For TimelapseCam set white balance to SUNLIGHT Set date and time settings to local standard time on plant cams before initial use Avoid using daylight savings time Specific settings for the Stardot NetCam SC are included in PhenoCam Installation Instructions by Cory Teshera Sterne et al updated April 2012 Imprinting options for date time or camera are used if available on the specific camera For example TimelapseCam should be set to imprint camera name date and time on each photo Focusing Adjust focus manually if possible to obtain a sharp image it may be helpful to focus on a specific object in the image such as a branch For plant cams capture and examine a test image onsite using a laptop or digital frame then adjust focus as needed Wingscapes sells an 80 accessory for viewing photos Mounted and aimed webcams are focused on a sunny day with a nearby laptop connected to the camera s
137. be fairly effective tick repellant Monitoring staff are strongly encouraged to treat their clothing with permethrin prior to conducting monitoring Monitoring staff should carefully follow the application instructions on the spray bottles to ensure their safety Permethrin will remain active for several weeks and through several washings e Monitoring staff should take additional precautions to protect themselves from ticks including tucking pants in socks and tucking in shirts Long sleeves and gaiters have been found to help e Check clothes and skin for ticks at the end of every field day Ticks typically need to be embedded for at least 24 hours for disease transmission to occur therefore the earlier ticks are found and removed the lower your chances are of acquiring a tick borne illness e If you find a tick that is already embedded use fine tipped tweezers to firmly grasp the tick close to your skin Slowly and steadily pull the tick s body away from your skin Be careful not to crush the tick s body to minimize the chances of it regurgitating fluids into the wound Clean the bite area once the tick is removed with soap and water e If you receive a deer tick bite notify the park Natural Resource manager who will help you start a worker s compensation CA 1 claim to get a CA 16 If you start to notice symptoms of a tick borne disease use the CA 16 to get medical treatment e Keep an eye out for any early symptoms of tick borne diseases
138. bring into line with other NETN protocols Updated Wildlife Acoustics website and software options 110 SOP 6 Deployment and Maintenance of Autonomous Recording Units Appendix S6 A ARU Deployment Datasheet Equipment Olympus ARU Equipment Song Meter Writing utensil Writing utensil Empty SD or micro SD card Empty SD card s Spare Olympus ARU windscreen Spare Song Meter windscreen Key to Olympus ARU locks if used Phillips 2 screwdriver to open and close units 4 D cell batteries Charged 12V or 4 D cell batteries Packets of silica desiccant 5 16 socket or nut driver for 12V battery case Packets of silica desiccant Date Location Park Site Serial Lat Long Circle one Initial Deployment or Maintenance Deployment Circle one Olympus ARU or Song Meter SM1 or Song Meter SM2 For Olympus ARU For Song Meter Preset 1 Start 3 Stop Recording Start Time Preset 2 Start 1 Stop Preset 3 Start 2 Stop Schedule File First file name New Empty Used Full Card 1D GB circle one Card 1D_ GB circle one Olympus SM Slot A 4 8 16 32 4 8 16 32 SM Slot B 4 8 16 32 4 8 16 32 SM Slot C SM2 only 4 8 16 32 4 8 16 32 SM Slot D SM2 only 4 8 16 32 4 8 16 32 For Maintenance Deployments only Notes e g any signs of disturbance or recorder problems Checklist ___ Take out the old 12V or D cell batteries and replace with a fresh 12V o
139. bystoma maculatum Spring peeper Pseudacris crucifer Wood frog Rana sylvatica Eastern tent caterpillar Malacosoma americanum Ovenbird Seiurus aurocapillus White throated sparrow Zonotrichia albicollis Winter wren Troglodytes hiemalis Spruce fir forest onl Bobolink Dolichonyx oryzivorus Red winged blackbird Agelaius phoeniceus Monarch butterfly Danaus plexippus Common loon Gavia immer Wood frog Rana sylvatica Common loon Gavia immer Great black backed gull Larus marinus The size of monitoring sites varies depending upon the habitat and species to be monitored For sites in which only plants are monitored the site should encompass the area immediately around the plants and conditions should be relatively uniform within the site For sites in which animals are monitored the site should encompass a walking route from which one can see or hear the species of interest USA NPN recommends that sites should be no larger than 6 hectares about 15 acres or 250 x 250 meters This upper limit constrains sites from being larger than a MODIS pixel In an open grassland or near a body of water a site might be the maximum recommended size 15 acres because it is possible to identify animals that are far away In contrast a site in a forest would probably be smaller because it would not be possible to identify species at large distances Even if it is possible to identify animals over a large area the area must b
140. cancellation of field work If return will be delayed contact RM DI before agreed upon check in time to establish a new check in time Always carry at least one method of communication and verify that it has a full charge before starting field work Emergency Not knowing emergency procedures Know who to contact and how to reach them in Preparedness Not having emergency supplies the event of a life threatening or non life threatening emergency Have current CPR and first aid certification Carry a well maintained first aid kit 55 SOP 1 Safety Potential Hazards Recommended Action or Procedure General foot Falling or tripping due to wet areas e Use caution at all times Walk carefully watching travel poor footing uneven terrain footing loose rolling rocks and heavy pack e Wear appropriate boots for conditions Stay aware of your feet Address blisters and hot spots promptly e Avoid carrying excessive weight loads or unbalanced loads e When walking on a steep slope lean upslope Appendix S1 B Job Safety Analysis continued aare alive and can rry cep E relying on them e Use extreme caution traversing wet rocks streams steep slopes or blowdown areas Working outdoors Being struck by falling trees or Listen to the weather forecast each morning park during storms branches being struck by lightning radio and or internet Plan or adjust field work to avoid being out in thunderstorms Postpone work if safety
141. ce USA National Phenology Network Tucson AZ 85721 U S Geological Survey Vermont Cooperative Fish and Wildlife Research Unit Burlington VT 05405 Department of Organismic and Evolutionary Biology Harvard University Cambridge MA 02138 July 2013 8U S Geological Survey National Coordinating Office USA National Phenology Network Tucson AZ 85721 U S Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins Colorado The National Park Service Natural Resource Stewardship and Science office in Fort Collins Colorado publishes a range of reports that address natural resource topics These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management including scientists conservation and environmental constituencies and the public The Natural Resource Report Series is used to disseminate high priority current natural resource management information with managerial application The series targets a general diverse audience and may contain NPS policy considerations or address sensitive issues of management applicability All manuscripts in the series receive the appropriate level of peer review to ensure that the information is scientifically credible technically accurate appropriately written for the intended audience and designed and published in a professional manner This report received formal h
142. cessing ae eee ea re ee net ees ese re ERE Re See et ME EEE eon ee ern tie ate 15 End of Season Proced r s Leninen tla ae ea etal i laa a a a Sa 15 ill Contents continued Page Data Management Analysis and Reporting x ccnccdoccsakas sdaled scssaeie seiadesdnvoangseeadeideisaaddeseiateadaulebia 17 Data Submission and Management 2 usvedsce sexes ccs aeesuvas eres Qotacdesavadedatataresgs toed anateen races 17 Quality Assurance Quality Control ccceececceesecsseceseceeeeeeseecsaeceseeneeeeeaeecsaecneeeeeeenseeesaeens 17 Data Analysis Integration and Reporting 0 0 0 ces ceseeseeceeseeeeeceseceeeeseeeseeeeeeseceaeceaesaeeeaeeeeees 17 Personnel Requirements and Trainin 244 3 is ed badecanscts seed ssadacthestetetelaadouqathaeeeiseatadte ate laaboaaeaeass 19 Roles ANE SMONSTO LLG ue Secigs ta as tas Sas oa aa lahol ce tele ales oS A Salah a Se ot alan a 19 A FUATITICATONS 2 ox ta tesne ch cap a E a a AA ARE E A A eon EAEE 19 Framing Procedure sinehan ia iao n TEI E A E OE EE Ea 19 Operational Requirements Ss isrennss eiri aa E EEEE R RO A R E RARE RETE 21 Annual Workload and Field SCHCCUIC sic sc chncsesercpecasaivnsgesandeeeaneahaeretaacgtaniersagah neces eeeaivle 21 Equipment and Supplies a Loe loc saclece ce sectes p eceut ae secctacaucedeh os Sacceous ocaat aeeenceeaaeraecyancene Meuse 22 Startup Costs and Budget ISSues x ic cssteindscaccta snsy saelap ad cctacbaetaqpdesdectvastedeagannsectecuslaude scan sbavss 22 Leal Requirements
143. change or set of changes tied to an updated version number Revision History Log Version Date Revised by Changes Justification 1 00 July 2010 Geri Tierney Adapted from NETN Forest Protocol SOP 1 00 Brian Mitchell 1 01 April 2011 and Geri Tierney Editorial changes 253 Ellen Denny Edited references to USA NPN Editorial 1 02 Jan 2013 Geri Tierney changes 254 The Department of the Interior protects and manages the nation s natural resources and cultural heritage provides scientific and other information about those resources and honors its special responsibilities to American Indians Alaska Natives and affiliated Island Communities NPS 962 121697 July 2013 National Park Service U S Department of the Interior MARK SERVICE Natural Resource Stewardship and Science 1201 Oakridge Drive Suite 150 Fort Collins CO 80525 www nature nps gov EXPERIENCE YOUR AMERICA
144. cies Two options for ARUs are available in this protocol building home made ARUs and using commercial ARUs the Wildlife Acoustics Song Meter Home made ARUs are a fraction generally less than a quarter of the cost of a commercial ARU and can serve as an excellent project for high school students that integrates physics electronics and ecology The drawback for these units is a less robust microphone and limited scheduling options Commercial units like the Song Meter come ready to use and have more flexible recording options more robust microphones customer support and a generally higher reliability The drawback for these units is the cost about 600 without memory cards or batteries Parks that are interested in using ARUs may choose which ARU option they want to deploy Sampling Frame and Site Selection Phenology monitoring occurs in NETN parks where resource management staff are able to coordinate monitoring activities for their park Some level of phenology monitoring has occurred in nine NETN parks ACAD APPA BOHA Marsh Billings Rockefeller National Historical Park MABI Morristown National Historical Park MORR Roosevelt Vanderbilt National Historic Sites ROVA Saugus Iron Works National Historic Site SAIR Saratoga National Historical Park SARA and Weir Farm National Historic Site WEFA The remaining NETN parks Minute Man National Historical Park MIMA and Saint Gaudens National Historic Site SAGA may c
145. cking once the prompt in the gui changes Select lower right corner of on rectangle with a left click 143 SOP 7 Acoustic Template Creation 50 100 150 200 250 300 Shift 39 120 No overlapped cells 580 pe 100 No empty cells 7 39004 Amplitude cutoff 31 w MEWE Pre i ea ale Pe rar he FTS 60 Frequency kHz 3 N EO EL 40 F A Ad Lhd UL 20 Time s Figure S7 14 Call 2 Rectangular area selection The reduced density appears as a dotted matrix of on points Right click to end on point selection or left click on the spectrogram to add additional on point rectangles After right clicking the prompt in the gui changes again Select upper left corner of off rectangle with a left click Right click to exit After the first left click a new prompt appears Select lower right corner of off rectangle with a left click All points in the matrix between the two selected corner points are designated as off points 144 SOP 7 Acoustic Template Creation 50 100 150 200 250 300 Shift 39 120 No ladles ie cells 100 80 60 Frequency kHz 40 20 0 5 1 1 5 2 2 5 3 3 5 Time s Figure S7 15 Call 2 after off point selection with a 3 point buffer Right click to end point selection or additional off points can be selected by selecting additional rectangles Automatic point selection This third option will automatically cast all overlapped cells
146. coustic Analysis bird Recordings s6 wav s7 home jkatz3 Dropbox UVMacoustic Analysis bird Recordings s7 wav t lim L list c 1 4 4 5 c 1 4 1 select click name SOSP_click_midphrase_B 138 SOP 7 Acoustic Template Creation 50 100 150 200 250 12 Shift unt 0 120 bad No overlapped cells pa 5888 i 100 gt 8 N empty cals i i ite Bel a a Beyo ry 80 S 4 K SU TE S 60 J 4 40 2 20 0 5 1 1 5 2 2 5 3 Time s FigureS7 8 Call 1 the first clip is displayed as dark gray the second as light gray and regions of overlap above the designated amplitude threshold are black These two Song Sparrow songs share an introductory phrase but not an ending phrase s6 wav ym s7 wav a ot r wt 8 j 8 i A ity i f 74 P oe TS i T i EIUN i T ia fra oy Jara iiaii Tea mie a mle Figure S7 9 The two Song Sparrow spectrograms in call 1 viewed individually Without overlaying them it is not obvious that the pair of introductory notes are not a perfect match The first task is to adjust the amplitude cutoff to include only the amplitudes that correspond to the syllables of the two songs In this example the amplitude cutoff is too low a lot of background noise is displayed and our goal is to only display the syllables of the song so the first adjustment is to raise the cutoff The R gui displays instructions on how to do this Amplitude cutoff selecti
147. creased from 317 to 580 The next step is on point selection The R gui again provides instructions on how to do this Point by point point selection Select on points with left mouse click When done right click 141 SOP 7 Acoustic Template Creation 50 100 150 200 250 300 12 Shift 10 39 No overlapped cells 580 3 8 No empty cells 7 39004 j Amplitude cutoff 31 oe iy d pye A i 4 iin ae a eat chi 2 y Frequency kHz cop Ta tt tor tik 0 5 1 1 5 2 2 5 3 3 5 Time s 120 100 80 60 40 20 Figure 7 12 Call 1 after on point selection The on points should fall within the black spectrogram which is composed of syllables common to both sound examples but it is not necessary to select all black cells nor is it necessary to select black cells from all syllables Next is off point selection The R gui has instructions for this as well Select off points with left mouse click When done right click 50 100 150 200 250 300 12 Shift joel 2ee No overlapped cells 580 pe 7 8 No empty cells ee Sony 39004 f Amplitude cutoff wi enpa 31 ai iin ere eo fm ete ete Frequency kHz Oo 0 5 1 1 5 2 2 5 3 3 5 Time s Figure S7 13 Call 1 after off point selection 142 120 100 80 60 40 20 SOP 7 Acoustic Template Creation Rectangular point selection An alternative to choosing just a handful of on or off points is
148. cs website at http www wildlifeacoustics com support download software The files can then be converted to forms other than WAV if necessary using the same audio tools listed above for the Olympus unit 109 SOP 6 Deployment and Maintenance of Autonomous Recording Units Revision History Version Date Revised by Changes Justification 0 10 March 2011 Corinne Brauer Jon Katz Original Version of Deployment and Maintenance of Autonomous Recording Units Brauer and Katz September 2011 1 00 March 2012 Geri Tierney Jon Katz Reformatted Made specific recommendations for standard NETN monitoring Added revision history Editorial changes 1 11 Dec 2012 Geri Tierney Reformatted Revised unit and file naming Accepted time format as current US time for Sonority Specified Olympus ARU should record in whole hour units to facilitate file renaming Adjusted recording time to include SM startup time 1 12 April 2013 Brian Mitchell Geri Tierney Clarified that Olympus and Song Meter require External separate deployment procedures review Added info about tradeoffs between Olympus and Song Meter units Added section on camouflaging labeling units to the Song Meter deployment section ARU testing should be a few weeks prior to deployment in case units need repair Other minor changes to address comments Editorial changes 1 13 July 2013 Ed Sharron Editorial edits to
149. csv dir C Users jkatz3 Desktop MetadataFolder loc prefix MABI02 ext mp3 CardRecorderID 1 duration 600 mins between 50 index hour kbps 128 samp rate 44100 channels 2 The index argument can be changed to time0 to subsample starting from the first 10 minutes of each recording rather than the top of each hour Files will be renamed to a user specified six digit location prefix followed by the original file s date modified including the time zone The name will be PARK HHH YY YY MM DD HHMMSS TZX mp3 Description of arguments to mp3Subsamp l 2 3 10 11 12 13 CardRecorderID This is the unique number assigned to each combination of card recorder and date deployed in the field Example 101 ext This is the file type of the recording wac wav or mp3 Example wac include the apostrophes as this is a text string loc prefix This is the eight character site id E g LOCA0001 include the apostrophes as this is a text string The first four characters are the NPS acronym corresponding to the park of deployment e g ACAD and the next four characters are the four digit number assigned by USA NPN for the site of deployment from This is the location of recordings on the SD card This is usually not in the top directory of the card but may be in a subdirectory named Data or Recordings Example F Recordings include the apostrophes as this is a text string to This
150. curring in that park Table S2 1 Core and optional habitats for phenology monitoring within NETN parks Core habitats are shown in bold The two core habitats are widespread and ecologically important within most NETN parks ACAD APPA BOHA MABI MIMA MORR ROVA SAIR SAGA SARA WEFA Vernal pools x x xX X X x x x x Northern hardwood x x x y forest Spruce fir forest X x Alpine and subalpine X Grassland and Open x X x x X x X Fields Permanent freshwater x x wetland Coastline xX x 1WEFA does not have true vernal pools but does have pools where amphibians breed Within these habitats fifteen plant species and twelve animal species are recommended for monitoring Table S2 2 Staff at participating parks choose species from the recommended list that are of interest and present in accessible locations at their park As a guideline NETN suggests each park focus on only four or five key species per park in order to obtain a sufficient number of observations per species focusing first on key species in core habitats We focus network wide efforts on a short list of selected species in order to provide sufficient data to determine trends Site selection At each park at least three sites are designated for phenology monitoring within each monitored habitat A site is the area which is searched for a monitored animal species and which encompasses any plants selected to monitor Sites are selected and setup by program sta
151. d trained monitors submit observation data directly online at Nature s Notebook www nn usanpn org The USA NPN has created this online interface to provide a user friendly method to record and store phenology observations and metadata Entries into Nature s Notebook are stored in the National Phenology Database and are freely available for others to access Raw data from automated audio and camera recorders are retrieved periodically by park staff or trained volunteers as described in SOP 6 Deployment and Maintenance of Autonomous Recording Units and SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras SOP After data are subsampled only Olympus ARU data and processed as described in SOP 8 Automated Sound Analysis and SOP 10 Processing Image Data processed datasets are stored by the NETN data manager until those files can be submitted via Nature s Notebook As of 2012 USA NPN plans to expand their data submission capabilities in the future to include data from automated recorders Quality Assurance To insure the quality of monitoring data collected in this program we rely on standardized written protocols and datasheets careful training for monitors making repeated observations and oversight by park level coordinators For digital data collection we employ standardized file naming procedures see Data Stewardship below and data imprinting on imagery for assurance that site and date metadata are correct
152. database section Next convert the wac files to wav files This conversion should be done promptly to ensure that the database matches the actual files For this step it is necessary to leave R and use software provided by Wildlife Acoustics The application Kaleidoscope performs this step in bulk and it offers the option to split the tracks and or cut the file into shorter length segments If one channel is dedicated to ultrasonic recording it will be necessary to split the channels but only the right channel will be logged in the database or csv file After converting the files to wav call fileCopyRename again to move the files to the survey folder but this time set metadata only TRUE to turn off the file renaming surveymetadata lt fileCopyRename from C Users jkatz3 Desktop TestFolder to C Users jkatz3 Desktop Surveys csv dir C Users jkatz3 Desktop MetadataFolder loc prefix MABI02 ext wav metadata only TRUE Olympus units Olympus units record in mp3 or wav format They are currently limited to three scheduled recording events per day to collect more than three surveys per day they should be set to record as many as 24 hours per day see SOP 6 Deployment and Maintenance of Autonomous Recording Units and then individual surveys of a fixed duration are subsampled from each hour of the recording Function mp3Subsamp is used to extract short surveys from continuous recordings and it simultaneously moves survey fi
153. dback to guide future monitoring During the off season network staff prepare and send an annual Resource Brief to all participating volunteers This Brief provides a descriptive summary of the annual implementation and any preliminary results of interest 16 Data Management Analysis and Reporting Data Submission and Management This protocol collects three types of raw data tabular observations digital audio files and digital image files Observation data are submitted directly by observers to the National Phenology Database via USA NPN s online interface Nature s Notebook www nn usanpn org Entries into Nature s Notebook are stored in the National Phenology Database and are freely available for others to access The data may also be viewed in visualizations available online Maintaining accurate standardized and informative file names plays a pivotal role in managing the large number of digital files generated by the implementation of this protocol Naming conventions for raw data files are described in the Data Management and Quality Assurance Quality Control SOP All computer data files are stored in duplicate to guard against data loss from hard drive failure For most data this is accomplished by storing identical mirrored copies on two separate external hard drives For raw image files this is accomplished by storing one copy on an external hard drive and a second copy on the PhenoCam server Processed data files fro
154. dedicated storage required A 1TB drive should be able to archive over 5 000 hours of mono wave files If the average song is three seconds long a location has 10 recorders deployed and 40 species are present at a location as many as 17 000 song events per species per site may be archived on the TB disk 176 SOP 8 Automated Sound Detection and Classification The tables below indicate roughly how many hours of survey recordings can be condensed to fit ona 1 TB disk assuming a single song duration for all species Estimated condensed survey hours 2 second song duration Species site gt fs 41667 20833 13889 10417 8333 6944 20833 10417 6944 5208 4167 3472 13889 6944 4630 3472 2778 2315 20 10417 5208 3472 2604 2083 1736 o 235 8333 4167 2778 2083 1667 1389 Estimated condensed survey hours 3 second song duration Songs hour Species site gt o 5 27778 13889 9259 6944 5556 f 4630 20 69a saz 2315 17365 f 1389 f 1157 o 2s do ossse 2778 1852 139 1m 96 Estimated condensed survey hours 4 second song duration Species site gt 5 10 15 2 ts 30 PS 20833 1017 f 6s4 5208 4167 3472 Songs hour Ss 8 10417 1736 pa on c e C s Extracting binding and verifying events listed in data tables The function bindEvents is designed to read in a data table of start and stop times from a csv file such as the output from Wildlife Acoutics Song Scope so
155. der Song Meter units are programmed to record hourly for a 10 minute interval or continuously depending upon the species and phenophases of interest Olympus units have limited programming options and are set to record continuously Units are visited at regular intervals for maintenance and data collection as described in the Deployment and Maintenance of ARUs SOP Digital time lapse photography is used to track seasonal development of individual plants and vegetation canopies Two types of automated camera may be deployed in participating parks 1 outdoor webcams cameras directly addressable via Internet Protocol and 2 plant cams inexpensive outdoor time lapse cameras targeted at hobbyists Cameras are programmed to capture images regularly during daylight hours as described in the Selecting Deploying and Maintaining Automated Digital Cameras SOP Plant cams are visited regularly for maintenance and data collection Data Processing As soon as possible after collection raw data files from plant cams are renamed as described in the Data Management and Quality Assurance Quality Control SOP Renaming incorporates critical information directly into the filename to help ensure accurate data stewardship Prior to data processing audio data files are subsampled if necessary and renamed using an automated procedure to obtain an hourly subsample as described in the Automated Sound Detection and Classification SOP Only the subsampled data i
156. desolder the existing wires attached to the power port These go to the voltage regulator Solder the wires to the These come from board before attaching the connector the diode Be sure the green go to the s terminals red to m and black to 2x4 hole pattern in board This is a small diode steady hands help When installed it should look something like this 117 SOP 6 Deployment and Maintenance of Autonomous Recording Units Appendix S6 D Building an External Power Cable for an SM1 or SM2 Recording Unit continued Add the voltage regulator to an SM1 or SM2 SM1 Solder the 4 black wire from the bridge rectifier to the GND center pin of the switching voltage regulator Solder the red wire from the bridge rectifier to the Vin pin of the voltage regulator Solder the 3 black wire from the bridge rectifier to the negative terminal of the battery holder Cut a 3 length of red wire and strip 1 4 of insulation from each end Solder one end to the Vou pin of the voltage regulator and the other end to the positive terminal of the battery holder Test for short circuits and test that the bridge rectifier channels input power to the positive pole only When testing shows satisfactory performance use the mounting tape to stick the voltage regulator to the side of the battery holder and replace the battery holder back in the case and screw it down SM2 Similar to inst
157. ding Adjusted text to remove untrained observer method Added to author list Reordered appendices Removed repeat photography SOP this is now an option referenced in camera SOPs Updated sample size section Updated methods for 2012 to match US NPN changes Selected black backed gull as recommended species Added Safety SOP Revised author list Added acknowledgements Removed target time for animal search Numbered SOPs Formatting and editorial changes Moved Observer Manual to accessory doc Reinserted untrained observer method Updated sections on automated sensors and data management Added Executive summary Edited references to USA NPN Clarified monitoring frequency Added overview of full acoustic data process Clarified PRA Privacy Act compliance Split Automated Sound Detection into 2 SOPs with separate SOP for Template Creation Editorial changes Editorial changes 30 Every other day monitoring is only needed during periods of rapid change Response to review and formatting changes Appendix A Monitored Phenophases for NETN Species NETN monitors phenology using phenophases defined by the USA National Phenology Network USA NPN These phenophases vary by species lifeform and were revised by USA NPN for 2012 During pilot seasons NETN monitored phenophases recommended by USA NPN at that time which differ from those shown here Specific definitions of each phenophase are found on specie
158. ding to the instruction manual as close as possible to the official U S time at http www time gov timezone cgi Eastern d 5 java You will need to temporarily install 4 D cell batteries to set the time or you can connect an SM2 to an external power supply of 6 5v 25v DC 30v DC can be used ifa 1kQ load resistor is added to the circuit 100 SOP 6 Deployment and Maintenance of Autonomous Recording Units Prepare Units Camouflage the units using brown and green spray paint before Property of deployment to reduce the visibility of the equipment Additionally National Park each unit must have a unique identification number permanently Service assigned and engraved or otherwise permanently affixed to it We use the Song Meter serial number as this ID number to assist with Northeast Temperate documenting potential equipment problems and facilitate deploying Network units at the same site each year Each unit is also labeled with a sticker ____ identifying the organization deploying the units and a request not to Please Do Not Disturb tamper with units See example at right with dummy contact number The contact phone number is the NETN Program Manager s number For information call 802 457 3368 x37 for network units or the Park Coordinator s 555 656 3011 number for park owned units It may also help to include the NETN web page for phenology monitoring for people interested in more information http science natur
159. documentation will assume that the MySQL database is located on a network or the cloud 181 Database Entity Relationship Diagram pkRecorderID INT fidManufacturer VARCHAR 45 gt fidMode VARCHAR 45 fidYearPurchased YEAR gt fidOperationStatus ENUM fH fidSerialNumber VARCHAR 45 gt fidComments VARCHAR 45 pkOrganizationID INT fidOrganizationName VARCHAR 145 fidAddressLinel VARCHAR 145 fidAddressLine2 VARCHAR 145 fidCity VARCHAR 145 gt fidState VARCHAR 2 fidZip VARCHAR S gt fidOfficePhone VARCHAR 12 gt fldOfficeEmail VARCHAR 125 fkPersonID INT fidContactInfo VARCHAR 45 gt fidContactType ENUM 3 pkLocationID INT 9 fidLocationName VARCHAR 100 fidLocationNameAbbreviation CHAR 6 fidLatitude DOUBLE fidLongitude DOUBLE gt fidDatum ENUM 9 fidLocationType ENUM pkSurveyID INT fkCardRecorderID INT fidSurveyLength FLOAT fidOriginalDateModified DATETIME fidTimeZone CHAR 43 fidOriginalRecordingName VARCHAR 256 9 fidSurveyName VARCHAR 256 O fidRecordingFormat ENUM fidSampleRate INT fidBitsperSample INT fidChannels TINYINT 1 pkResultID INT fkSurveyID INT fkTemplateID INT O fkPersonID INT fidDateTime DATETIME fidTimeZone CHAR 3 fidTime FLOAT fidScore DECIMAL 5 3 fidHit TINYINT 1 fidVerified TINYINT 1 fidAnalysisTyp
160. dow makers storm branches damaged trees with large broken limbs and unstable standing dead trees Do not spend extended time in an area with hazard trees Carrying a pack Injuries from improper packing Learn how to properly pack adjust lift and carry and other adjustment and lifting of backpacks a pack equipment Injuries from improper carrying of When hand carrying gear keep one hand free gear If carrying long equipment be aware of other people and never swing around quickly Avoid allowing a long piece of equipment to project up and behind you where you cannot see it General operation Injuries from vehicle accident Perform pre operational check of vehicle oil tire of a vehicle Damage to vehicle pressure tire condition fluids wipers brakes lights gas etc Report all needed repairs to the crew leader or supervisor promptly Do not use the vehicle if it is unsafe Wear seat belts with shoulder harnesses whenever vehicle is in motion Do not use cell phones or text while driving Only NPS employees volunteers or authorized cooperators and contractors are allowed to operate or ride in a government vehicle Ensure full visibility from all windows and mirrors Clean windshield regularly Always ride inside the vehicle Properly store and secure all tools equipment and cargo so that they will not shift during sudden starts or stops Plan your travel before you start Know your route Practice defensive driving be alert
161. ds of rapid change if possible but not less than weekly Observers record data onsite using datasheets and then submit data online into Nature s Notebook as described in the NETN Phenology Observer Training Manual Park staff or specially trained volunteers maintain automated equipment and download data at regular intervals as described in the SOPs Making Observations At each site individual plants and animal populations are observed for phenological status and intensity or abundance using phenophases defined by USA NPN Appendix A as described in the Observation SOP During each visit monitors record one of these options for each phenophase e y if the phenophase is occurring e n if the phenophase is not occurring e if observer is uncertain whether the phenophase is occurring If observers did not check for a particular phenophase they are instructed to not choose any of the three options and leave the phenophase blank For most phenophases observers also record intensity or abundance using quantitative measures defined by USA NPN Instructions for recording intensity or abundance are included on Nature s Notebook Phenophase Definitions sheets Abundance is recorded as an actual count in some cases or as an estimate a percentage or a class variable in others as specified in the USA NPN Phenophase Definition sheet for that species For example if birds are seen feeding then observers count and record the actual number
162. e ENUM COR BIN fidLikelihood DECIMAL 4 4 gt fidPosterior DECIMAL 4 4 fidCutoffValue DECIMAL S 3 pkArchivelD INT fkSurveyID INT gt fidDateTime DATETIME 9 fidArchiveType ENUM lt Dashed lines indicate relationships one side indicators are considered equivalent lt Crows foot indicates many side of relationship gt fidTemplateName VARCHAR 96 fidRecordingDate DATETIME fidRecordingEquipment VARCHAR 9 fidClipPath VARCHAR 255 fldSampRate INT gt fidPtOnT LONGTEXT fidTStep DECIMAL 16 16 gt fidFrqStep DECIMAL 8 8 fidNTBins INT 11 9 fidFirstTBin DECIMAL 26 16 fldNFrqBins INT 11 2 fidDuration DECIMAL 16 14 9 fidFrqLim VARCHAR 45 O fidFFTwi INT 5 O fidFFTovip INT 2 9 fldFFTwn VARCHAR 45 9 fidScoreCutoff DECIMAL 6 4 gt fidTemplateType ENUM BIN COR gt fidActive TINYINT 1 ponunuo aseqeyep TOSAN Sunearp y gs xIpueddy UOTeOTISseyD pue uoTO9 aq punos powuony 8 dOS SOP 8 Automated Sound Detection and Classification Appendix S8 A Creating a MySQL database continued Set Up a Cloud Database Your organization may have a server that allows the creation and storage of a MySQL database For instance at the University of Vermont affiliates can create a database at http webdb uvm edu There are many cloud database services and we ll be describing one called Xeround https cloud xe
163. e Partner Organization then from the next window choose Northeast Temperate Network then choose a specific park ACAD APPA BOHA MABI MORR ROVA SAIR SARA or WEFA Then Nature s Notebook NCO staff notify the park coordinator that a new group member wishes to join and the coordinator must recognize and accept the member before access is granted Park coordinators use the Manage Users link in Nature s Notebook to view information about group members Informational Displays At some monitoring sites informational displays may be used to attract park visitors to make one time or initial observations Poster displays and or handouts provide USA NPN information on the species and phenophases to be monitored at that site and Nature s Notebook datasheets are provided These materials are self explanatory to enable one time observers to make a contribution without training Sites with informational displays must be registered in Nature s Notebook as public sites rather than shared sites so that any visitor is able to submit an observation for that site Data Collection Data describing the site is collected during plot setup by park staff or cooperators using the Site Datasheet found in Appendix A below and entered online into USA NPN s National Phenology Database using Nature s Notebook Data describing an individual plant is collected whenever a new individual is selected and marked for monitoring Plant reg
164. e database the results automatically associate with the proper survey based on the survey name Send all pks dbUploadResult detection obj BINpks what peaks analysis type BIN Send hits from findPeaks to tblResult default is what detections dbUploadResult detection obj BINpks analysis type BIN Archiving Surveys and Hits Archiving Surveys The storage volume necessary to archive full survey files is substantial but it opens the door to future reanalysis as algorithms improve NETN will store all surveys used during analysis SongMeter recordings will be archived as WAV files and subsampled Olympus surveys will be archived as MP3 files 175 SOP 8 Automated Sound Detection and Classification Archiving detections as WAV clips If full surveys are archived it is not necessary to archive detections separately but in other cases it is recommended to archive event detections Archiving event detections has a number of advantages beyond simply providing evidence of a species presence including the ability to resolve future taxonomic splits Although NETN will be archiving full survey files making archiving detections unnecessary it may be helpful to store some example files for each species to save having to reconstruct examples from file names and locations of detections within each file The function to export the hits in a series of hits only spectrograms is collapseClips The output will be a single WA
165. e divided into different sites if it includes habitats that are obviously different For instance if making observations at a pond in a meadow the pond and the meadow must be registered as separate sites At BOHA an island may be considered a single site Due to the use of volunteer monitors and the high sampling frequency needed for phenological observation sites are selected for convenience of access and presence of monitored species as well as lack of human disturbance representation of local conditions and uniformity This approach allows NETN to detect temporal trends in phenological change for key species at these index sites NETN assumes temporal phenological trends at index sites are indicative of change at other locations within these park habitats However it will not be possible to extrapolate data from these index sites to other locations using this non random sample design This is a significant limitation of the selected sample 66 SOP 2 Site Selection and Set Up design but one which is warranted in this case The selected index site design meets NETN sampling objectives to detect temporal change while accommodating the need to monitor conveniently located sites Staff use the following criteria to select sites for phenology monitoring Convenient Sites must be convenient and accessible enough to visit at least weekly throughout the growing season and in all weather An ideal location for a designated site
166. e fields columns that compose them Tables begin with the prefix tbl followed by a word that describes the content of the table The fields also begin with prefixes that include pk for primary key a value unique to each record in the table fk for foreign key a value that refers to the primary key in another table and fld which indicates that the field stores data Each table is dedicated to storing information about only one aspect of the data For example a table called tblPerson stores information about people involved in the acoustic monitoring program These may include people who deploy and operate recording devices people who run analyses etc A table called tblLocation stores information about the locations in which acoustic recordings were made including latitude and longitude the location name and whether the location is the location of a monitoring site or whether the location is a place where only a template has been recorded The table called tblResult stores the results of the analysis The tables required to create a database compatible with this package are listed below A full description of the database including an Entity Relationship diagram and full schema are in Appendices S8 A and S8 B OOS ON SE ot m RS Re RK DO ABRWNrR CO TABLE NAME tblCard tblCardRecorder tblRecorder tblLocation tblSurvey tblTemplate tblResult tblSpecies tlbArchive tblPerson tblPersonContact tblOrganization
167. e flooding Editorial changes 1 11 May 2012 Geri Tierney Revised to remove casual observers Updated intensity category example for 2012 Use of binoculars in tall trees encouraged 1 21 Sept 2012 Geri Tierney Removed detailed description of NPN data collection referring instead to current data sheets Added USA NPN recommended Nature s Notebook text Added patch monitoring instructions Editorial changes 1 22 Nov 2012 Geri Tierney Reinserted one time or initial observations by untrained observers 1 23 Jan 2013 Ellen Denny Edited references to USA NPN Clarified Frequent Geri Tierney monitoring frequency Editorial changes monitoring only needed during rapid change 79 SOP 5 Building an Autonomous Recording Unit Northeast Temperate Network Version 1 00 Overview Automated audio recording can be an important data source for long term phenological research providing a consistent and objective stream of data at optimal frequency in both accessible and remote locations This protocol includes two options for implementing automated audio recording 1 using commercial autonomous recording units ARUs the Wildlife Acoustics Song Meter and 2 building less expensive ARUs using off the shelf components The choice of whether to implement automated audio monitoring for phenology and which recording option to use is up to the individual parks Commercial devices are more convenient more powerful and come with a ce
168. e left soft key labeled 24H Press and release the OK button when done Record the SD or micro SD card number on the Deployment Datasheet Each card must be assigned a unique number which should be written on the card with permanent marker to assist with linking data to the correct recorder during downloads and trouble shooting problem cards Calculate the start and stop times for each 8 hour recording in 24 Hour time on the ARU Deployment Datasheet Appendix A Use a start time that is close to the current time but that provides enough time to program all three recordings Five minutes should be sufficient Press and hold the OK button for two seconds to open the main menu Scroll down to the Rec Menu microphone icon and press OK Program the first recording period for a discrete number of hours i e x hours and 0 minutes a Highlight the Timer Rec option and press OK b Highlight Preset 1 and press OK c In On Off select ON press OK d Set the Day to Everyday and press OK e In Time set the start time calculated on the deployment datasheet a few minutes after the current time Set the stop time calculated on the datasheet 8 hours after the start time or some other discrete number of hours and press OK Verify that the times match your datasheet f Set the Rec Mode to MP3 128 kbps and press OK g Inthe Folder option select microSD Press OK then accept the default Folder A and pres
169. e minimized Park level coordinators interact with observers during training and provide observer support By doing so they are able to correct potential errors as well as provide some insight into the skill of different observers Quality Control Data validation is made by comparing phenological data from multiple methods at the same site and at related sites i e similar sites at the same park Data collected by untrained and trained volunteers and from automated cameras and audiorecorders will be compared to identify possible bias introduced by method by training or lack or training by frequency of collection and by species or phenophase observed During training park coordinators identify volunteers whose skills or experience are demonstrably higher than typical volunteers or alternatively who are newer or less experienced than typical volunteers Park coordinators keep a simple record of volunteer skill levels as 1 beginner 2 typical and 3 advanced this record is updated annually for returning volunteers as skills improve over time This information on observer skill level may be used during data analysis to give greater or lesser weight to data collected from higher or lower skilled observers respectively In order to do so the NETN Data Manager may need to submit lists of volunteers in each class to USA NPN NCO staff and request a sorted list of corresponding observer identification numbers in each class This procedure will en
170. e nps gov im units netn monitor programs phenology phenology cfm To prepare units for attachment to trees install four 3 piece of perforated steel tape in a loop to the back of each unit one at each corner using 6 x 32 x 3 4 bolts a washer and two nuts The units already have a hole to accommodate the bolts at each corner The choice of internal or external power is up to the individual parks When sites are close to roads external batteries can be a significant time saver since they reduce the frequency of maintenance visits However the weight of these batteries means that D cells may be better for deployments that are some distance from roads Keep in mind that when using rechargeable D cells one bad battery can significantly reduce deployment time Batteries should be individually numbered and if a recorder stops early then all four should be carefully tested SM1 units have no external power supply port but for extended deployments it is possible to add one that includes a waterproof connector reverse polarity protection and a switch voltage regulator See Appendix D for details An external power supply cable can be purchased through Wildlife Acoustics Inc or constructed separately to allow an SM2 or modified SM1 to draw power from a 12V battery The SM2PWR cable by Wildlife Acoustics dissipates surplus power above 5V as heat but the switching regulator used in Appendix D will keep that power available and can be as much as 4
171. e other conductor and shield to the L terminal of the male phono plug check to be sure that each conductor maintains the proper channel throughout all connections Solder the shield to the terminal Assemble the housing over the connections Seal the holes where the audio connector exits the Pelican case with waterproof glue and allow to dry Use the ohm meter to test for connectivity between all three contacts of the phono plug there should be none Left The outer insulation removed Right The mylar shield open Left The stereo phono plug contacts Right The plug after soldering R A 7 gt 58 LAAT Zip style 4 cable L ties _ EE 5 8 3 8 Hole pattern in Pelican Case floor 85 SOP 5 Building an Autonomous Recording Unit Prepare the windscreen shell Cut a rectangle of hardware cloth 9 5 x 5 5 Trim one of the 5 5 edges flat and leave tails on the other 5 5 edge Trim the 9 5 edges in the same way Cut a separate square of hardware cloth 3 x 3 Bend the rectangle into a cylinder 3 in diameter and 5 tall bend the cylinder so that the resulting circular strands of the mesh are on the outside of the straight strands so that the cage will easily slip onto the holder Use needle nosed pliers to bend the wire tails around the mating edge to lock the edges in place Trim the square piece of hardware cloth so it is roughly a circle
172. e the on points from the off points in a binaryPtMatch analysis gt plot BINtemplates Waiting to confirm page change Waiting to confirm page change Waiting to confirm page change Template BTNWd10BIN Template BTNWd10Buff2BIN Frequency kHz T 0 5 1 18 2 25 Os 1 15 2 2 5 Time s Time 5 Template BTNWd10Buff3BIN Template BTINWd0S5Buff2BIN Frequency kHz 05 1 15 2 25 05 1 15 2 25 Time s Time s FigureS8 1 The off points in the template should ideally be restricted to just noise but in the top left image with no buffer it includes some lower amplitude signal as well This may inhibit the ability of binaryPtMatch to distinguish between signal and noise by reducing the difference between the mean on point amplitude and mean off point amplitude A buffer of 2 top right pushes most of the off points to the edge of the signal and a buffer of 3 bottom left satisfactorily restricts the off points to just noise In this example increasing the buffer above 4 will allow for the wiggle that may accommodate subtle variations in song timing or frequency between individual birds The bottom right image illustrates a template with a buffer of 2 and a density of 0 5 167 SOP 8 Automated Sound Detection and Classification Analysis of Audio Files The next step is to analyze a survey file with one or more templates to determine if specific target species occur in the survey This process searches
173. eR 2 plyr 3 RODBC for connecting R to a database See Appendix S8 C in SOP 8 Automated Sound Detection and Classification for instructions on downloading R and selected packages Audacity is a free audio editing application which provides a useful tool for viewing sound files audacity sourceforge net Audacity works on MacOS Windows and Linux operating systems and can be installed as a zip file which is helpful if you are on a computer with restricted permissions Before working in Audacity set these default preferences In the Edit menu choose Preferences select Spectrograms from the list on the left and check the box to Show the spectrum using grayscale colors Set the default window size to 1024 Close the preference panel Set Audacity to open files in spectrogram view by clicking Tracks in the list on the left and setting the Default View Mode to Spectrogram Click OK A WAV file player is needed during template construction to verify that results sent from R are the target sound of interest Use a pre installed player e g Windows Media Player in Windows Quicktime in MacOS or Rhythmbox in Linux or use a dedicated cross platform player that can be opened via the command line through R such as wv_player exe or SoX Note that if you choose to use Windows Media player the application name you will pass to R is wmplayer exe while Ubuntu s Rhythmbox is rhythmbox wv_player can be downloaded at
174. earch Unit at the University of Vermont 81 Required Materials SOP 5 Building an Autonomous Recording Unit a Suggested Estimated Qty Description source Item URL Cost Olympus DM 420 Digital Voice B002JTX87W http www amazon com Olympus Digital Voice 99 99 42 Recorder Recorder DM 420 dp BO02JTX87W OR OR Amazon com OR OR Olympus DM 620 http www amazon com Olympus 142665 DM 620 149 00 Digital Voice 142665 Voice Recorder dp B004S561V0 Recorder a http mouser com ProductDetail Eagle Plastic 2 oD WB 24AWG Mouser com 12BH121A GR Devices 12BH121A GR qgs sGAEpiMZZMupuRtfu7 2 62 LDS GC 252bdUGrIKBfc93ebWmxALgLTw 3d http mouser com ProductDetail Kobitone 254 ECM640 RO qs sGAEpiMZZMsYQx 2 Microphones Mousercom 254ECMB40 RO PYEnGVuKI20UawXrSZjjuYNZ7QPDw 3d o omnidirectional PaE OR Super Circuits PAS PASIL http Awww supercircuits com accessories microphone 19 98 s super high gain micro audio system pa3 a EAk a a http mouser com ProductDetail Alpha Wire 2400C 0 1 Cable 2C 24AWG Mouser com 602 2400C 100 SL005 qs sGAEpiMZZMsa6 252bU7AAQG5bpaG 3 55 SHIELD 100 UlY64uY ZIQNJ9ZOBQ0 3d Phone Connectors http www mouser com ProductDetail Kobiconn 171 2 PHONE 3 5MM Mouser com 171 PA3291 1 E PA3291 1 E qs XuGxlpNJLiglU7CKCfGhgnU 1 00 MONO QdZJgeDw8XnstEAEwm0g 3d http www mouser com ProductDetail Kobiconn 161 1 A E a M
175. ected signal amplitude and background noise level to be determined Note any difference and do not use the mic if it does not meet established criteria a large difference in the recorded dB value and actual value to be determined It may be possible to adjust gain settings on the Olympus recorder to calibrate a microphone that does not initially meet the criteria Set Date and Time The time and date used by each unit are set in advance and synchronized among units using the Olympus Sonority Software which is included with the recorder Install the software if it is not already installed then connect the Olympus ARU to your computer using the USB cable included with the device Set your computer time to match the time with the official time at http www time gov timezone cgi Eastern d 5 java and then open Olympus Sonority In the Device menu select Synchronize Date Time and press OK After disconnecting the recorder from the computer be sure to set the unit to 24 Hour time by pressing and holding the OK button for two seconds opening the Device Menu and selecting Time amp Date and then pressing the podcast button once The recorder ID is customized by selecting Transmit User ID in the National Park Device menu the first four characters of the user ID will appear as a prefix to each file recorded by the device Our naming convention is to Service assign each recorder the four digit USA NPN site number Northeast Te
176. ed effects of stressors or elements that have important human values In addition to APPA NETN encompasses Acadia National Park ACAD the Boston Harbor Islands National Recreation Area BOHA and 10 national historical parks and national historic sites in the Northeastern United States This protocol was developed in collaboration with the USA National Phenology Network USA NPN Organized in 2007 USA NPN is a nation wide partnership among federal agencies schools and universities citizen volunteers and others to monitor and understand the influence of seasonal cycles on the nation s biological resources Participants in the network collect share and use phenological data models and related information USA NPN promotes broad understanding of plant and animal phenology and makes phenological data and related information freely available to scientists resource managers and the public to aid in decision making and adaptation to changing environmental conditions Toward that end the National Coordinating Office NCO of the USA NPN promotes the use of standardized approaches to monitoring phenology and maintains a national phenology information management system including Nature s Notebook USA NPN s online plant and animal phenology observation program www nn usanpn org USA NPN monitoring standards were developed with extensive input from participating organizations Both the USA NPN data infrastructure and their standardized monit
177. eld season In the early spring each year park staff review designated monitoring sites selected individual plants and walking routes This review ensures that sites and plants still meet selection criteria as described in the Site Selection and Setup SOP and that sufficient numbers of sites and individual plants of each species are selected Site and plant marking is updated or replaced as needed Park staff or cooperators re deploy and field test all automated equipment cameras and audio recorders in use at that park Establishing sites It is critical that each monitoring site and monitored plant be marked with a unique identifier In cases when multiple observers are monitoring the same site or plant this unique identifier will be used to combine observations Following the guidelines outlined in the Site Selection and Setup SOP staff at each participating park establish specific procedures for marking sites and plants that are aesthetically acceptable at that park These marking procedures are used by park staff and cooperators to establish designated sites for multiple observers and automated sensors Information describing each site is collected prior to the commencement of monitoring as described in the Site Selection and Setup SOP This information is collected during site setup by the park staff or cooperators Site information is updated annually or if conditions change Park staff setup and maintain shared sites for trained obs
178. elop approaches to mitigate those hazards All monitoring staff must review safety procedures in the Volunteer Training Manual and sign an acknowledgment that they have read the JSA in Appendix B First Aid Kits and Training NETN strongly encourages all monitoring staff to carry a backpacking first aid kit with them in the field An inventory of first aid kits should be performed prior to each field season to ensure that all medical supplies are in sufficient quantity and haven t expired Each first aid kit should have an inventory list of the supplies it should contain Items in first aid kits that are used should be promptly replaced If you do not have access to a first aid kit and want to carry one let the park Natural Resource Manager know and NETN will purchase one that can be borrowed from the park NETN also strongly encourages all monitoring staff to obtain basic first aid and CPR training particularly if they have not been certified in the past 5 years Teamwork NETN recommends that people work in teams of two or more for monitoring at sites which are off trail or at remote or hard to access sites Working with another person makes it more likely that someone will be able to obtain help in the event of an accident and working with someone else usually makes field work more enjoyable If you are unable to find someone to work with you and you would like to work with someone else please notify the park Natural Resource 38 SOP 1
179. ence across years showing the positive or negative difference in days on the X axis and year on the Y axis 4 We expect our methods to yield sufficient data for analysis of phenology of individual plants however if insufficient data exists for individual plants data may be pooled by species at a site 246 SOP 12 Data Analysis and Reporting Trend statistics Trend analysis will occur every 5 years after 10 years of data are available A 20 year dataset is typically regarded as the minimum length for phenological trend analysis so the 10 and 15 year reports will be preliminary Trend analysis will be performed using a linear mixed model in the R statistical package using the Ime function in the nlme package or other software selected by NEIN To detect trend over time for a specific phenophase event for a species pooled across sites or for group of species hypothesized or observed to exhibit similar phenological shifts regress event date on year If pooling species include species as a random effect For plant phenophases include individual plant within site as a random effect for animal phenophases include site as a random effect This simple analysis looks only for long term trend over time to determine if measurable phenological shifts are occurring If sufficient data from widely spaced parks exist include latitude as a fixed effect omitting site if necessary Next to detect trend per degree C or unit growing degree
180. ept 32kHz compressed up to 16kHz mono and band triggered up to 8khz mono 113 SOP 6 Deployment and Maintenance of Autonomous Recording Units Appendix S6 B Unit Specifications continued e 70 75mA when recording compressed up to 48kHz except 32kHz and band triggered up to 24kHz mono e 80 90mA when recording 32kHz and up to 48kHz compressed and band triggered up to 44 1kHz mono e 90 100mA when recording band triggered up to 48kHz mono e 110mA when recording band triggered up to 48kHz stereo e Separate power for time of day clock uses 2 AA size batteries lt 0 1milliamps 2 3 year service life SMX IT Microphones e Enclosure NEMA 4X weatherproof e Sensitivity 36 4dB 0dB 1V pa 1KHz e Frequency response flat 20Hz 20 000Hz e Signal to Noise Ratio gt 62dB e Directionality Omnidirectional Memory Capabilities Recording Times in Hours Mono 1 channel 48 000 44 100 32 000 24 000 22 050 16 000 8 000 4 000 2GB 5 8 6 3 8 7 11 6 12 6 17 4 34 7 69 4 4GB 11 6 12 6 17 4 23 1 25 2 34 7 69 4 138 9 8GB 23 1 25 2 34 7 46 3 50 4 69 4 138 9 277 8 16GB 46 3 50 4 69 4 92 6 100 8 138 9 277 8 555 6 32GB 92 6 100 8 138 9 185 2 201 6 277 8 555 6 1111 1 64GB 185 2 201 6 277 8 370 4 403 1 555 6 1111 1 2222 2 128GB 370 4 403 1 555 6 740 7 806 2 1111 1 2222 2 4444 4 Stereo 2 channels 48 000 44 100 32 000 24 000 22 050 16 000 8 000 4 000 2GB 29 3 1 4 3 5 8 6 3 8 7 17 4 34 7 4GB 5 8 6 3 8 7 11 6 12 6 17 4 34 7 69 4
181. equentially display all hits in the specified time bounds Press esc to abort the verification process Note that the boundary box corresponds to the template time limit and the bandpass filter limits View the output by viewing the detection list CORdetections lt getDetections CORpks BINdetections lt getDetections BINpks 173 SOP 8 Automated Sound Detection and Classification Verifying correlation results with annotated survey spectrograms The SpecScorePlot function saves a series of fully customizable annotated spectrograms as PNG files The output of SpecScorePlot does not need to be assigned to an object Instead specify the spectrogram frequency limits the duration of each spectrogram in seconds a location to save the graphics files and a hit marker type specScorePlot detection obj CORpks flim c 0 10 scorelim c 0 1 t each 60 file name Dropbox LabDemo _scc_MABI2_A_062510_ hit marker points The resulting PNG files will be numbered sequentially so the first 60 second spectrogram specified with the t each argument will be scc_MABI2_A_062510_001 PNG the second will be SCC_MABI2_A_062510 002 PNG etc An example file looks like this Frequency kHz BTNWd1 0 BTNW partial 0 8 4 BTNWd 8 Score 300 310 320 330 340 350 360 05 00 05 10 05 20 05 30 05 40 05 50 06 0C Time s Verifying binaryPtMatch results with annotated survey spectrograms Verify t
182. ervers and or automated sensors and public sites for any site at which untrained observers will submit data on the Nature s Notebook website to allow multiple observers to submit observations at designated park sites as described in the Site Selection and Setup SOP Individual plants are selected and marked for observation by park staff and by volunteer monitors if allowed at that park as described in the Site Selection and Setup SOP Park staff confirm correct species identification of all monitored plants At some designated monitoring sites informational displays may be used to attract park visitors to make one time or initial observations Poster displays and or handouts provide USA NPN information on the species and phenophases to be monitored at that site and Nature s Notebook datasheets are provided These materials are self explanatory to enable one time observers to make a contribution without training These sites must be designated as public sites in Nature s Notebook to allow park visitors to submit data online 13 Sequence of Events During the Field Season Once the field season begins staff at each participating park or APPA region support volunteer monitors Observers create accounts online in Nature s Notebook www nn usanpn org and download a Nature s Notebook datasheet package including Phenophase Definitions sheets for each monitored species Observers visit their sites every other day during perio
183. esignated sites in participating NETN parks using the phenophases datasheets and infrastructure provided by the USA National Phenological Network USA NPN with some modification as described herein Observations are made by two groups of monitors a park visitors recruited onsite to make one time or initial observations and b trained volunteers or staff who submit repeat observations These data are used to determine trends in phenological change for key species at index sites and assist park managers with the detection and mitigation of the effects of climate change on park resources Observers submit data online directly into Nature s Notebook www nn usanpn org Nature s Notebook is an online plant and animal phenology observation program of the USA National Phenology Network Equipment and Supplies e A Nature s Notebook datasheet packet including Phenophase Definition Sheets and Datasheets for each monitored species an Animal Checklist if observing animals and Cover Sheets for each site from www nn usanpn org or from park coordinator at BOHA only Clipboard optional and pencil Binoculars optional but encouraged for observing animals and tall trees Park approved plant marking equipment for first trip if allowed to select plants Map of site if provided by park Photo guide to phenophases BOHA only Procedure Park visitors may be recruited onsite by informational displays to make one time or initial observations in par
184. ess setting it to FALSE allows you to quickly flip through spectrograms of the hits without verifying and the player argument identifies the WAV player that will receive the play commands Spectrogram cross correlation scores will range between 0 and 1 so set the 171 SOP 8 Automated Sound Detection and Classification scorelim argument to those values If using binaryPtMatch the scores typically range between 0 and 40 so use those values instead CORpks lt showPeaks detection obj scc which one BTNWd1 0 scorelim c 0 1 verify TRUE player play 1 True detection Enter y or n 1l y 1 TRUE 12 7 10 5 Frequency kHz Correlation coefficient Time s BINpks lt showPeaks detection obj scores scorelim c 0 40 verify TRUE player play 1 True detection Enter y or n 172 SOP 8 Automated Sound Detection and Classification TRUE 124 Frequency kHz o o l A oO _ 534 Oo E v 5 E Oo 2 amp 2 a eet E tee Nicene cence cee o E a a T1 T2 73 74 Time s Running these commands will bring up the graphics above and the R console will offer the option to mark it as a true detection press y and ENTER a false detection press n and ENTER or play the clip using the previously specified player press p and ENTER If unsure you can enter na or NA and ENTER The hit number is noted at the top and R will s
185. established trails They also set up explicit check in times for visits to remote or hard to access locations so if a search is initiated after a missed check in the individual should be located within a few hours of starting a search A score of 6 was assigned for this worst case scenario Team Selection The monitoring protocol identifies the essential skills and abilities required to execute this protocol in a competent manner but one of the features of this protocol is that significant experience is not required Monitoring staff may have limited experience with research and field work and many of them are retirees There is also variation in their orienteering and hiking experience Monitoring staff are strongly encouraged to obtain basic first aid and CPR certification and to work with a partner if they are at all concerned about field conditions A score of 6 was assigned because some monitoring staff may have limited experience with off trail hiking and navigating Team Fitness The nature of the Phenology Monitoring Protocol should ensure an overall high level of team fitness The monitoring itself is not difficult or time consuming although significant travel hiking time may be needed for some parks and sites especially ACAD and APPA A score of 3 was assigned because the monitoring does not take long even though hiking to the sites or routes can be strenuous Monitoring staff must be diligent about adequate rest and nourishment to en
186. etter select notes or syllables that are common to each In this process two example clips are visually overlaid upon one another to identify regions of overlap This process works most effectively when the two song examples have reasonably high or at least very similar signal noise ratios As with binary point template construction from a single clip the amplitude threshold is selected first then the user slides the first clip over the second until they are aligned as desired and finally on and off point identification proceeds with either click rectangle or automatic selection The template will store only the path to the second clip for future plotting Single point selection Manually selecting a handful of on and off points will offer the greatest speed advantage and a lot of flexibility to include or ignore acoustic features but to achieve the increased speed some template selectivity will be traded To begin this process assign the output of the makeBinTemplate2 function to an object This function requires two clip paths to songs with identical sampling rates that are joined in a list and the time limits a list of vectors with the min and max time for each clip set for each clip must be of equal duration Frequency limits are a single vector for the spectrogram and set select point Call 1 two Song Sparrow clips using click selection SOSP_click_midphrase_B lt makeBinTemplate2 clip L list s6 home jkatz3 Dropbox UVMa
187. evolved species e Species with critical early spring phenophases such as spring wildflowers and amphibians e Species of special interest to park managers or visitors This list of key species will be updated periodically as new information becomes available Staff at participating parks choose species from the recommended list that are of interest and present in accessible locations at their park As a guideline NETN suggests each park focus on only four or five key species per park in order to obtain a sufficient number of observations per species focusing first on key species in core habitats For plant observations individual plants are marked and observed as described in the Site Selection and Setup SOP At least three individuals of each plant species are monitored at each site in order to document variability in phenophase occurrence within the population Variability within individuals in a population can exceed variation among populations Brugger et al 2003 Goulart et al 2005 Monitoring the same individuals repeatedly over time offers several advantages over monitoring a population Most importantly it limits the influence of confounding factors such as genotype and microclimate that might affect observations of different individuals over time Additionally sampling multiple individuals in a population will allow us to draw statistical inferences about the population Individual plants are selected following USA NPN guideline
188. ext strings that describe the location or a feature of the site When a site is registered online into the USA NPN s National Phenology Database using Nature s Notebook the site is assigned a unique four digit identification number which is used to identify this site during data analysis and for data management of audio and image data files Selection of Individual Plants Individual plants are selected for monitoring by program staff or cooperators or by volunteer monitors if allowed at that park At each site at least three individual plants of each monitored species are selected for monitoring Observing three individuals at each site is best for understanding how phenology varies among individuals at a site Individual plants are selected following these USA NPN guidelines Selected plants should appear to be healthy undamaged and free of pests and disease Selected plants should also not be closer than 6 meters about 20 feet to a road or building Selected plants of the same species at a site should be growing in a similar environment but not be direct neighbors or closer than two to three times the width of the plant s canopy In a forest selected trees should occupy similar positions in the canopy and habitats on the ground 67 SOP 2 Site Selection and Set Up If observing annual plants which only survive one growing season or biennials such as garlic mustard which survive for two growing seasons the first or the
189. ey should make sure their colleague knows where it is carried Be alert to potential hive and nest locations while hiking to plots and working on plots Look for insects travelling in and out of one location e g brush ground holes and hollow logs If someone is stung Benadryl and a cold compress may bring relief If stinger is left behind scrape it off of skin Do not use tweezers as this squeezes the venom sack worsening the injury If the victim develops hives asthmatic breathing tissue swelling or a drop in blood pressure seek medical help immediately Black Bears Black bears range throughout the Northeast and along the entire Appalachian NST but an encounter with a bear in the field is not likely since bears generally avoid people Nevertheless be alert for bears near dawn or dusk and be especially aware of mother bears with cubs Never approach cubs or come between a mother bear and her cubs If a bear is encountered face the animal and continually make noise do not freeze or remain silent Appear larger by standing tall waving arms or jacket over your head and slowly back away Never run from a black bear if charged or attacked throw objects and shout loudly and fight back aggressively 46 SOP 1 Safety Vehicle Safety Responsibilities of Vehicle Operators Virtually all monitoring staff for the phenology protocol will be using their personal vehicles to get to and from their monitoring sites Monitoring staff are
190. ff or collaborators However in some cases volunteers may collaborate with park staff to identify sites that are both convenient and 65 SOP 2 Site Selection and Set Up appropriate for monitoring At each site multiple methods may be used and multiple observers contribute observations at most sites In some cases automated monitoring occurs at sites which are also observed by volunteer monitors this provides a useful quality control check on volunteer observations However sensitive or hard to access sites may be monitored by automatic recording only Table S2 2 Plant and animal species recommended for monitoring within NETN core and optional park habitats Core habitats are shown in bold Habitat Plants Animals Vernal pools Northern hardwood forest Spruce fir forest Alpine and subalpine Grassland and Open Fields Permanent freshwater wetland Coastline Garlic mustard Alliaria petiolata White wood aster Eurybia divaricata Sugar maple Acer saccharum Red maple Acer rubrum Bunchberry Cornus canadensis Painted trillium Trillium undulatum Hobblebush Viburnum lantanoides Balsam fir Abies balsamea Common milkweed Asclepias syriaca Rough stemmed goldenrod Solidago rugosa Red maple Acer rubrum Marsh marigold Caltha palustris Purple loosestrife Lythrum salicaria Beach pea Lathyrus japonicus Beach rose Rosa rugosa Rockweed Ascophyllum nodosum Spotted salamander Am
191. ftware or an object downloaded from the database This function will extract just the events from the survey which can then be saved individually or they can be saved as a single file of many clips tied together Before using the data table in the function the file must be edited so that all times are in decimal seconds and at a minimum there must be 1 a column of start times with the heading tStart 2 a column of end times with the heading tEnd 3 acolumn identifying the species with a heading Species Optionally there can also be a column identifying the file of the recording with the heading FileName Use bindEvents by assigning its output to an object in R event rec lt bindEvents rec E users jkatz3 Desktop BTNWtemplates SARA3_A_062610 wav file SongScope ExampleEventList csv by species TRUE parallel FALSE 177 SOP 8 Automated Sound Detection and Classification The output from bindEvents is a list of WAV files with an element for each species Setting by species FALSE will result in a list of one WAV file containing all events As written above a summary of the species contained can be viewed by checking the names of event rec gt names event rec 1 AMCR AMGO AMRO BAWW BINW CEDW COYE GCFL GRCA OVEN 11 REVI RWBL SCTA SOSP WAVI WIWR YWAR And the WAV recordings themselves can be written to disk as a single file pe
192. g tool Hacksaw Sewing machine or needle and thread Volt ohm meter Prepare the Pelican case Drill a 7 32 hole through both long ribs on the hinge side of the box Place the hole at least 1 8 from all edges centering the hole 5 8 from the end of the rib and 4 from the side should provide sufficient support Pass the steel rod through the hole and use the swaging tool to crimp both ends so it cannot slip back out of the hole Only a small amount of mushrooming is necessary to keep the rod in place This preparation will 83 SOP 5 Building an Autonomous Recording Unit provide an anchor for fastening the case to a tree or other support Prepare the recorder support Insert two deck screws through the lauan or plywood backboard into the 2x2 support fastening the length of 2x2 to the lower left corner of the lauan and leaving 1 8 along the left margin Cut a 2 5 length of Velcro strap in half lengthwise to form 1 2 wide straps and use a small screw to fasten one end of each Velcro strap to the 2x2 support 3 4 from the top on the left and right sides Repeat this and fasten two more straps 3 4 from the bottom on both sides Prepare the battery holder Stack two battery holders end to end both with the wire leads pointing down Pass the leads from the top holder through the lower holder so that the leads of both emerge from the lower holder Cut two segments of Velcro strap 9 long and place o
193. haps not as user friendly as commercial software the algorithms are easy to explain and visualize have many fewer parameters to worry about when trying to build templates and have been shown to be accurate for identifying many species The approach is implemented on a free widely used platform R and because the basic algorithms are not being changed over time old data does not need to be reanalyzed unless a new species template is developed The R platform and package we have developed definitely has a learning curve but so does the process of building recognizers in Song Scope This SOP provides specific instructions for creating templates to use in automatic sound detection It was developed by Jon Katz for use by the NPS Northeast Temperate Network Phenology Monitoring Program SOP 8 Automated Sound Detection and Classification describes the overall process of managing audio files and analyzing them with existing species specific templates and the R package monitoR that has been developed for automated sound recognition 119 SOP 7 Acoustic Template Creation Software Programs Used Sound detection is performed within R a freely available language and environment for statistical computing and graphics which can be downloaded from the Comprehensive R Archive Network http cran r project org Before using R for spectrogram cross correlation or binary point matching add these packages to your R library 1 tun
194. he results using the showPeaks SpecScorePlot and collapseClips function as described in the sccCor verification section Be aware when specifying a scoreLim value that sccCor will produce a correlation plot in which values are in the set 0 1 but with binaryPtMatch the difference between mean on and off values will be plotted which should range within the set 0 40 specScorePlot detection obj BINpks flim c 0 10 scorelim c 0 40 t each 60 file name Dropbox LabDemo _bin_MABTI2_A_062510_ hit marker points 174 SOP 8 Automated Sound Detection and Classification 10 F 8 gt 6 i G4 o g 2 0 40 BTNWd1 0BIN BTNWpoint1 0BIN 30 Z BTNWauto SBIN g S 20 N 10 0 300 310 320 330 340 350 360 05 00 05 10 05 20 05 30 05 40 05 50 06 00 Time s Storing Results Ina CSV file To write a csv of the table you wish to store use getPeaks or getDetections to retrieve all peaks or just detections Assign the output to a new object CORpeaks lt getPeaks CORpks BINpeaks lt getPeaks BINpks CORdetections lt getDetections CORpks BINdetections lt getDetections BINpks Save the output file by writing it to a csv write csv BINpeaks file E users jkatz3 Desktop BINWpeaks csv write csv BINdetections file E users jkatz3 Desktop BTNWdetections csv In the database The dbUploadResult function uploads the results either as all peaks or as just detections Once in th
195. henoCam network For this we need some basic information about your site including location contacts description of the vegetation at the site and in the field of view etc To do so please fill out the survey at the following URL http tinyurl com 7gd3ham With the information included we will set up a directory for you to transfer your images We try to use a convention for site name being a single lowercase string with no special characters e g morganmonroe The registration and management of the PhenoCam is administered by Tom Milliman at University of New Hampshire thomas milliman unh edu For future reference however problems with transmission and lost communications are mediated by Steve Klosterman at Harvard University klosterman fas harvard edu Image Filename Conventions Our automated image processing requires that the filenames follow a strict naming convention which allows us to extract the image date and time from the filename Our standard convention is sitename YYYY MM DD hhmmss jpg where YYYY 4 digit year MM 2 digit month DD 2 digit day of month hh hours mm minutes ss seconds We assume the date and time are for the local standard timezone We can handle variations in the file naming convention automatically so if the standard naming convention doesn t not work for your site please contact us thomas milliman unh edu and request an alternative Transferring Files Once the site is set u
196. henophase the data can be used to describe the temporal distribution of each phenophase e g Sparks et al 2005 which can be important for identifying potential phenological mismatches among species Miller Rushing et al 2010 In addition this approach allows integration of status and event based data because the timing of particular phenological events can be extracted from status based observations However the reverse is not true phenological status cannot be extracted from event based observations because they usually note only one date for each phenological event Another advantage of status monitoring is that interpreting and recording phenological status at any given time is typically easier for citizen volunteers than evaluating whether or not a phenological event has occurred on a particular date Many studies have shown the value of phenological observations made by non scientists for example Gazal et al 2008 Howard and Davis 2009 There are however species that are inappropriate for volunteers to monitor because they are difficult to identify or are dangerous e g rattlesnakes and bears Additionally some phenophases e g the instars of some insects breeding of secretive species are difficult for untrained observers to monitor Thus we will follow USA NPN recommendations for phenophases to observe these recommendations include consideration of difficulty and level of expertise needed Automated monitoring using ine
197. here to make amplitude comparisons for each potential detection these coordinates combine into something like a map The features of interest in the map are locations with signal and locations with noise These are saved as either on or off points where on points correspond to signal and off points to noise Constructing a binary template is a means of choosing the on and off points while looking at an example song clip for guidance Click Rectangle Automatic and Line Selections Use the args call to view the arguments for the makeBinTemplate function gt args makeBinTemplate function clip t lim c 0 Inf frq lim binary FALSE select click dens 1 buffer 0 spec cols spec palette amp cutoff i Where the allows the user to add FFT parameter arguments These arguments may include e wl to change window length e g wl 1024 must be a power of 2 Common wls are 128 256 512 and 1024 e ovip to change window overlap e g ovlp 50 must be a percent between 0 and 99 Common ovlps are 0 25 50 and 75 e wn to change window function e g wn hamming others include the default hanning blackman rectangle and triangle 132 SOP 7 Acoustic Template Creation Detection of some calls may be improved by changing the FFT window length FFT overlap or FFT window function The default FFT parameters are typically suited for vocalizations that
198. hoc calibration or correction but the reference panel is nevertheless important as a means of verifying day to day camera functionality The reference panel is easily made from a Carlon rectangular plastic electrical box cover Available at http www lowes com pd_130189 223 HB1BL_0_ spray painted with matte gray primer e g Rust Oleum 12 Oz Gray Primer Flat Spray Paint http www lowes com pd_89137 90 1680830 0_ The panel is re painted annually Figure S9 3 Sample image showing grey reference panel included in the camera field of view Verify that the panel is at least 20x20 pixels in size 209 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras For aerial cameras mounted on towers building roofs etc mount the panel on a horizontal pole on an adjustable mount such as a U Bolt at a distance of about 3 from the camera to panel One drawback of this method is that the panel will not always be illuminated the same as the canopy at which the camera is pointed For ground mounted cameras mount the panel on a vertical pole as close as possible to the vegetation of interest Verify that the size of the panel in the image is no smaller than 20 x 20 pixels In both cases the panel is mounted vertically The reference panel is included as a region of interest when analyzing images for seasonal changes in vegetation green chromatic coordinate gcc using PCIP software The gec of the reference panel should
199. hoose to participate in the future Within each park monitoring occurs at select sites in core or optional habitats designated for phenology monitoring Table 3 The two core habitats vernal pools and northern hardwood forest are monitored at all NETN parks except BOHA and SAIR which do not contain those habitats In addition park staff may choose to monitor optional habitats occurring in that park Table 3 Core and optional habitats for phenology monitoring within NETN parks Core habitats are shown in bold ACAD APPA BOHA MABI MIMA MORR ROVA SAIR SAGA SARA WEFA Vernal pools x x x x x x x x x Northern x x x x x x x x x hardwood forest Spruce fir forest x Xx Alpine and x subalpine Grassland and Open Field 5 x i x x x Permanent freshwater x xX x wetland Coastline x x WEFA does not have true vernal pools but does have pools where amphibians breed At each site multiple methods may be used and multiple observers may contribute observations Automated monitoring occurs at sites which are also observed by volunteer monitors this provides a useful quality control check on volunteer observations However sensitive or difficult to access sites may be monitored by automatic recording only Due to the reliance on volunteer monitors and the high sampling frequency needed for phenological observation sites are selected for convenience of access and presence of monitored species in addition to lack of human disturbance repre
200. hotgun Marantz species code c BINW BTINW BTNW BTNW BTNW This call demonstrates all arguments to send only one template dbUploadTemplates templates CORtemplates which one BTNW_rect_C db name acoustics uid username pwd sEcurePass2 analyst 2 locationID 9 date recorded 2010 05 29 recording equip SennheiserShotgun Marantz species code BTNW Building a Template Library and Fine Tuning Templates 148 SOP 7 Acoustic Template Creation Now your mission is to find more potential templates so you can choose the highest performing one To do this you will use spectrogram cross correlation and the sccCor function Rationally choosing sound clips for your template The compareTemplates function uses sccCor or binaryPtMatch to collect the score of each potential template against all other potential templates The compareTemplates function arranges the results into a list of four tables the first is a list of mean times for the hits that will be used as row names in the rest of the lists the second is a list of peak times for each template in seconds the third is a list of peak times for each template in mm ss ss and the fourth is a table of all scores for all templates This process will be demonstrated using sccCor but the process is identical for binary point matching if the function binaryPtMatch is used in place of sccCor To use compareTemplates run the sccCor functi
201. hoto above the recorder is shown with a brown microSD to SD adapter lying on the contro buttons This adapter is an option if microSD cards are not available in the capacity desired while SD cards are In 2010 32GB microSD cards were available for less than 70 and a 32GB SD card plus adapter cost 95 67 28 We observed that while the adapter made access for card changes easy occasionally the recorder would not recognize that a new card had been inserted into the adapter and many minutes were spent power cycling the unit attempting to reboot 88 SOP 5 Building an Autonomous Recording Unit Specifications Note Linear PCM is available on the Olympus DM 520 but not on the DM 420 used in this recorder Exterior High impact structural copolymer polypropylene Exterior Dimensions 8 12 x 6 56 x 3 56 20 6 x 16 7 x 9 0cm LxWxH Microphone Cable Length Variable Microphone Cable Shielded Yes Microphone Impedence 2 2 K Ohms Microphone Directional Properties Omnidirectional Microphone Operating Voltage 2 V Microphone Sensitivity 40 dB 3 dB Recording Formats Linear PCM MP3 WMA Recording Input Level Mic Sense Middle 60 dBv Recording Input Impedence 2 2 kQ Recording Power Input D cell battery 2 4 V 9 11 amps Recorder Operating Temperature 0 C 42 C 32 F 107 7 F Recorder Overall Frequency Response See table below Recorder Plug In Power 0 8 V 2 5V Microphone Frequency Response Overal
202. ice collaborated with USA NPN AMC and the Appalachian Trail Conservancy ATC to undertake a 3 year pilot phenology monitoring project in NETN parks Planning and data collection began in 2009 and continued through 2012 This pilot sought to Implement phenology observation at NETN parks providing a template for monitoring phenology in other parks throughout the United States Develop methods to train staff and volunteers in monitoring techniques Develop methods to manage data including collection storage and quality control e Educate NPS staff park visitors and the broader public Collect data to determine long term trends in phenology of selected species Determine correlations between phenological observations and climate data The pilot tested three methods of data collection recruiting park visitors to make one time observations training volunteers to make repeat observations and training staff to make repeat observations and primarily involved four NETN parks ACAD APPA BOHA and MABI The pilot experience helped the group better understand how phenology monitoring could be undertaken at different parks with different logistical needs and pools of potential monitors It also served as a useful field test of this evolving protocol A report describing the pilot project is available on the USA NPN website at http www usanpn org netnproject as are additional materials describing this collaborative pilot project Go
203. icer TCO Dave Schuller 215 597 5368 can be notified 6 In reporting an accident monitoring staff should state the facts to the best of his her knowledge Conclusions as to fault or responsibility should not be stated Monitoring staff should report the accident only to authorized representatives of the Government their insurance company and police officers investigating the accident Monitoring staff shall also file any report required by law 7 Get name and address of witness preferably two witnesses Ask witness to complete Standard Form SF 94 Statement of Witness if the form is available 8 State provide your name address place of employment or park where volunteering name of your supervisor park Natural Resource Manager if a volunteer and upon request show your driver s license and vehicle registration information 47 9 10 11 12 13 14 15 SOP 1 Safety Complete Standard Form SF 91 Motor Vehicle Accident Report as soon as practical If conditions prevent this make notes of the following a Registration information for other vehicle s owner s name owner s address tag number VIN and vehicle description b Information on other drivers name address operator s permit and expiration date c Name and address of each person involved and extent of injury in any d Name and address of company insuring other vehicle s and insurance policy number e General
204. icro SD Card 16GB micro SD Card 32GB micro SD Card ST XQ 132 h 264 h 528 h ST HQ 266 h 532 h 1064 h ST SP 532 h 1068 h 2136 h HQ 532 h 1068 h 2136 h SP 1048 h 2096 h 4192 h LP 2084 h 4168 h 8336 h Guide to Battery Life With NiMH Batteries Recording Mode 2 D cell Batteries 4 D cell Batteries PCM 48kHz 145 h 290 h MP3 128kbps 159 h 318 h ST XQ 159 h 318 h LP 203 h 406 h The standard recording format in NETN parks is 128 kbps MP3 Use of 4 D cell batteries is standard 90 SOP 5 Building an Autonomous Recording Unit 91 SOP 5 Building an Autonomous Recording Unit Revision History Version Date Revised by Changes Justification 0 10 Jan 2011 Jonathan Initial draft Building an Autonomous Katz Recording Unit Based on the Olympus DM 420 Digital Voice Recorder Katz Jan 2011 0 11 Feb 2012 Geri Tierney Reformatted Added overview and revision history Editorial changes 0 2 June Jon Katz Revised procedure to construct a two 2012 channel recorder for redundancy amp to match microphone power requirements 0 21 Oct 2012 Geri Tierney Editorial and formatting changes 1 00 April 2013 Brian Add text describing options DIY or Address Mitchell commercial ARUs and add option for external better microphones and recorders review comments 92 SOP 6 Deployment and Maintenance of Autonomous Recording Units Northeast Temperate Network Version 1 12 Overview Autom
205. igh level peer review based on the importance of its content or its potentially controversial or precedent setting nature Peer review was conducted by highly qualified individuals with subject area technical expertise and was overseen by a peer review manager Views statements findings conclusions recommendations and data in this report do not necessarily reflect views and policies of the National Park Service U S Department of the Interior Mention of trade names or commercial products does not constitute endorsement or recommendation for use by the U S Government This report is available from the Northeast Temperate Network http science nature nps gov im units netn monitor programs phenology phenology cfm and the Natural Resource Publications Management website http www nature nps gov publications nrpm To receive this report in a format optimized for screen readers please email irma nps gov Please cite this publication as Tierney G B Mitchell A Miller Rushing J Katz E Denny C Brauer T Donovan A D Richardson M Toomey A Kozlowski J Weltzin K Gerst E Sharron O Sonnentag F Dieffenbach 2013 Phenology monitoring protocol Northeast Temperate Network Natural Resource Report NPS NETN NRR 2013 681 National Park Service Fort Collins Colorado NPS 962 121697 July 2013 ii Contents Page Fables niaii sy tapas Ma ai e ae i lsc tig woapata dia a a E ata TAER vii Exec tiye SUM a a
206. ile format owned by Microsoft that is in widespread use sufficient to be considered cross platform As a result WAV files are playable on nearly all devices 121 SOP 7 Acoustic Template Creation Create an initial template To analyze your acoustic files you will need to create some templates A template is built from a recorded song example and provides the search image for the computer The recorded song must be a wav or mp3 file usually one that is clipped from a survey file or one that is recorded using a directional microphone There is a distinction between the recording and the template unlike the song clip the template will contain only the portions of the song clip to be used for analysis and it will contain information about the sampling rate the FFT parameters and the score cutoff that should be used with it Template files have extensions bt or ct and the song clips they are built from have extensions wav or mp3 Templates can be made once saved and used many times Templates are sampling rate and FFT parameter specific for example if you are using some mp3 recorders that sample at 44 1kHz and some Song Meters that sample at 24kHz it is necessary to either make a template for each sampling rate or to downsample the 44 1kHz files to 24kHz Similarly a template made from an FFT window length of 512 and a hanning window function can only be used at that FFT length If you are using a database each template is assigned
207. imate or other environmental variables in fact they can lead investigators to draw erroneous conclusions from the data Miller Rushing et al 2008a Also limiting monitoring to first events generally misses repeat events such as a second flush of leaves after a defoliation event and can be impractical for species in regions where the beginning of a season or an event is difficult to define Status monitoring as defined by USA NPN is the evaluation of phenological status over the course of the entire year using carefully defined phenophases Denny et al submitted A phenophase is a specific seasonal life history stage or behavior with a measurable duration such as the period during which a plant has open flowers or the period during which the males of a particular bird species can be heard singing their typical territorial song Using this approach observers record a plant or animal s phenological status during a series of repeat observations Observers may also include a count or estimate of intensity or abundance associated with the phenophase This status based approach is data rich because it provides information on presence absence and duration of phenophases The richness of the data will facilitate exploration of relationships between phenology and climate variables comparisons between the phenologies of interacting species and precise quantification of error Thomas et al 2010 By documenting the intensity or abundance of each p
208. imately linearly with an increase in the number of CPU cores scc lt sccCor survey C Acoustics Surveys MABI2_A_062510 wav template L CORtemplates parallel FALSE gt Sec A templateScores object Survey information Wave Object Number of Samples 14571815 Duration seconds 607 16 Samplingrate Hertz 24000 Channels Mono Stereo Mono Bit 8 16 24 32 16 Template information gt Fast Fourier Transformation Most NPS computers operate on the Windows Operating System but some parks may have other machines 168 SOP 8 Automated Sound Detection and Classification 7 sccCor templates original recording lower frequency BTNWd1 0 C Users jkatz3 Dropbox LabDemo Templates BTNW wav 3 656 BTNWpartial C Users jkatz3 Dropbox LabDemo Templates BTNW wav 4 547 BINWd 8 C Users jkatz3 Dropbox LabDemo Templates BTNW wav 3 609 BTNWd 5 C Users jkatz3 Dropbox LabDemo Templates BTNW wav 3 609 BINWd 2 C Users jkatz3 Dropbox LabDemo Templates BTNW wav 3 703 BTNWauto 8 C Users jkatz3 Dropbox LabDemo Templates BTNW wav 2 016 BTNWauto 2 C Users jkatz3 Dropbox LabDemo Templates BTNW wav 2 016 upper frequency lower amp upper amp duration n points score cutoff BTNWd1 0 6 797 86 965 0 000 25039 8160 0 4 BTINWpartial 8 438 92 442 0 000 23981 6014 0 4 BINwd 8 6 703 92 442 2 093 2 603 2108 0 4 BTNWd 5 6 797 82 282 2 098 2 560 2135 0 4 BTNWd 2 6 656 83 995 5 877 2 560 902 0 4 BT
209. imum frequency This approach balances the need for frequent observations with the recognition that volunteer monitors may not participate at optimum frequency Sites with automated cameras are monitored regularly throughout the day Sites with audio recorders are monitored hourly or continuously depending upon the species and phenophases of interest see Deployment and Maintenance of Autonomous Recording Units SOP for details Species and Individual Selection NETN has developed a list of key species recommended for phenology monitoring in NETN parks Table 1 and 2 To be suitable a species must be readily identifiable by trained observers or by automated acoustic or photographic techniques and exhibit observable phenophases In addition preference is given to species with legacy data sets available for comparison To be selected a species must be found within a designated core or additional selected park habitat and be of scientific or management interest in one of these categories e Foundation species dominant primary producers such as trees and shrubs which provide habitat for other species and exert large influence on the system 10 e Invasive species and insect pests which may be particularly responsive to climate change e Species vulnerable to phenological mismatch such as animal pollinated plants and their pollinators migratory or diadromous migratory between salt and fresh waters species and their key food sources and co
210. in causes flooding Pull the unit tight against a tree or post by two chains of plastic cable ties The cable ties pass through the metal loops at the corners of the cases and wrap completely around the tree or post Install a chain of cable ties at the top of the Song Meter unit and a chain of cable ties at the bottom of the unit If installing on a tree pass the 4 vinyl covered steel cable through the lower loops and around the tree and attach and tighten a cable clamp for security s y A BS er If using an external battery place the battery box at the base of the tree and connect the two hose clamps together at the ends to form a single longer hose clamp Pass the 8 cable around the base 106 SOP 6 Deployment and Maintenance of Autonomous Recording Units of the tree and loop the ends over the hose clamp Slip the long portion of the hose clamp under the battery box and place the battery in the box Securely connect the power cable to the battery and the Song Meter put the lid on the battery box making sure not to crimp the power cable and secure the hose clamp over the top of the box to hold it shut Open the Song Meter case and place two desiccant packets inside the unit SM1 only SM2 units have a moisture absorbing system Install the SD card with the programmed schedule in slot A and power up the Song Meter by pressing and holding the wake exit button for two seconds Press the select button and scroll down to the LOAD
211. incremented by decimals e g Version 1 06 to Version 1 07 when there are minor modifications that do not affect requirements or procedures included in the protocol Add rows as needed for each change or set of changes tied to an updated version number Revision History Log Version Date Revised by Changes Justification November 1 00 2012 Brian Mitchell Adapted from NETN Landbird Protocol SOP 1 New SOP 64 SOP 2 Site Selection and Setup Northeast Temperate Network Version 1 23 Overview Within each participating park phenology observation occurs in selected sites within core or optional park habitats NETN follows recommendations of the USA National Phenology Network USA NPN for site and individual plant selection with some modifications as described herein Due to the use of volunteer monitors and the high sampling frequency needed for phenological observation sites are selected for convenience of access and presence of recommended species as well as representation of local conditions Acceptable marking procedures vary by park Monitored habitats and species Within each park or APPA region monitoring occurs at select sites in core or optional habitats designated for phenology monitoring Table 2 1 The two core habitats vernal pools and northern hardwood forest are monitored at all NETN parks except BOHA and SAIR which do not contain those habitats In addition park staff may choose to monitor optional habitats oc
212. information such as location time measurements weather damage etc Encourage police to provide a Police Report and if available submit a copy with SF 91 If you have a camera take pictures of the accident scene and any damage to the vehicles involved Submit along with SF 91 If vehicle is unsafe to operate arrange for towing services if a government vehicle pay using the vehicle gas card Submit all reports and data to the park Natural Resource Manager within one working day If a federal employee or volunteer is injured the workers compensation process needs to be initiated within 48 hours of incident The park Natural Resource Manager will assist with this process It is important for injured monitoring staff to receive prompt medical treatment Make sure the employee sees a doctor not a nurse nurse practitioner or physician s assistant The park Natural Resource Manager will submit copies of all reports and data to the NPS regional TORT Claims Officer TCO Dave Schuller 215 597 5368 as soon as possible but no later than 10 calendar days after the accident Accident collision reports should be filed for l All motor vehicle accidents involving federally owned or leased vehicles and employee owned or rented vehicles while being used on official business regardless of the amount of damage All public visitor accidents will be reported on a SF 91 when a government owned vehicle is involved governmen
213. ing in one survey at a time 4 call sccDetect to perform sccCor and findPeaks on the survey and save the results 5 export just the clips for verification long term storage if necessary 6 open the next survey and repeat from step 4 For example to search for these three bird species Ovenbird oven Black throated Green Warbler btnw and Song Sparrow sosp Load your templates for these species using the bandpass filter values and cutoff values stored in the template templates lt makeTemplates wave L list oven F users jkatz3 templates oven wav btnw F users jkatz3 templates btnw wav sosp F users jkatz3 templates sosp wav dy frq lim L list oven c 3 6 9 btnw c 4 1 6 7 sosp c 1 5 7 dy score cutoff L list oven 0 30 btnw 0 41 sosp 0 28 179 SOP 8 Automated Sound Detection and Classification The first step of the batch processing is a simple one command item to list the directories recorderList lt list dirs F users jkatz3 FieldRecordings 20120912 Now we start looping through the recorder list starting with making a list of survey files for i in l length recorderList surveyList lt full names for j in l lengt RU survey lt r recorderNam recorder surveyName ext from list files recorderList i E h surveyList pattern wav adWave surveyList j lt tail strsplit surveyList j 1 2 get
214. installed in the recording unit fldDateCollected DATETIME NULL COMMENT The date that the card was retrieved from the recording unit PRIMARY KEY pkCardRecorderID CONSTRAINT fk_tblRecordings_tblPerson FOREIGN KEY fkPersonID gt REFERENCES acoustics tblPerson pkPersonID ON DELETE NO ACTION ON UPDATE NO ACTION CONSTRAINT fk_tblRecordings_tblRecordingUnit1l FOREIGN KEY fkRecorderID REFERENCES acoustics tblRecorder pkRecorderID ON DELETE NO ACTION ON UPDATE NO ACTION CONSTRAINT fk_tblRecordings_tblLocationl FOREIGN KEY fkLocationID REFERENCES acoustics tblLocation pkLocationID ON DELETE NO ACTION ON UPDATE NO ACTION CONSTRAINT f k_tblFieldRecordings_tblCardl FOREIGN KEY fkCardID REFERENCES acoustics tblCard gt pkCardID ON DELETE NO ACTION ON UPDATE NO ACTION CONSTRAINT f k_tblCardRecorder_tblPrograml FOREIGN KEY fkProjectID REFERENCES acoustics tbProject pkProjectID ON DELETE NO ACTION ON UPDATE NO ACTION ENGINE InnoDB COMMENT Track which surveys are recorded by which recorders via whic comment truncated CREATE INDEX fk_tblRecordings_tblPerson_idx ON acoustics tblCardRecorder fkPersonID ASC CREATE INDEX fk_tblRecordings_tblRecordingUnit1l_idx ON acoustics tblCardRecorder fkRecorderID ASC 196 SOP 8 Automated Sound Detection and Classification
215. int selection the on points are colored orange Bottom right call 1 after off point selection the on points remain orange and the off points are colored blue 136 SOP 7 Acoustic Template Creation Call 2 specifying a buffer BTNW_rect_d100_b2_B lt makeBinTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav t lim c 0 2 8 frq lim c 2 9 select rect buffer 2 binary TRU Call 3 using density and buffer arguments BTNW_rect_d20_b2_B lt makeBinTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav t lim c 0 2 8 frq lim c 2 9 select rect binary TRUE buffer 2 dens 0 2 Call 4 using the auto selection method BTNW_auto_d80_b2_B lt makeBinTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav t lim c 0 2 8 frq lim c 2 9 select auto dens 0 8 buffer 2 binary TRUE 20 40 60 80 100 120 9 l l l l l 20 40 60 80 100 120 BI H 180 p 8 180 160 8 4 4 160 2 140 74 e4 D 140 Sh ali 8 1205 67 5 3 120 es 597 S 3 10 3 54 3 100 uw 80 a 80 3 60 a 3 L 60 2 BA h 1 mn i l l i j f 0 5 1 1 5 2 2 5 Time s 20 40 60 80 100 120 9 i fi i L 180 180 8 z 160 160 77 i 140 140 a L 120 amp 120 oO v es 57 S 100 100 Ww uw call L go 80 34 L 60 60 2 T T T T T 0 5 1 1 5 2 2 5 Time s Time s FigureS7 62 Top
216. ion Version 1 00 Record when individual plants are selected for monitoring and enter online into USA NPN s Nature s Notebook Update annually or if conditions change Station code or site name Date recorded Plant 1 Plant 2 Plant 3 Species common name Nickname Patch y or n Y or N Y or N Y or N Patch size Patch size units sq ft OR sqm sq ft OR sqm sq ft OR sqm Shade status Wild Y N Y N Y N Watered Y N Y N Y N Fertilized Y N Y N Y N Gender M F Both M F Both M F Both Comments Nickname Assign a unique name or code to each plant to distinguish among them For example if you choose three red maple individuals at this site you could nickname them red maple 1 red maple 2 and red maple 3 Patch Is this a monitored patch Most NETN monitoring will be on individual plants but in some cases a patch may be monitored Monitoring a patch can be easier for plants where individuals are hard to distinguish such as groundcover and some grasses Patch size If monitoring a patch mark the corners of the patch and always monitor within the marked area Measure and record patch area as square feet or square meters Patch size units If monitoring a patch circle unit of measure used square feet or square meters Shade status Which of the following best describes the shade status of each individual For small plants and shrubs
217. ional ROI covering the reference panel and calculate g for the reference ROI The gec for the reference panel should be essentially stable over time It may be variable from day to day because of weather and clouds but there should be no long term or seasonal trend in the gec of the reference panel If a trend is detected in gcc for the reference panel ROI this trend must be taken into account during analysis of data from this camera and both the camera and reference panel should be carefully examined for degradation Filtering night time images Night time images are excluded from analysis in PCIP by filtering out dark images from around sunrise or sunset by simple RGB thresholding To do so ROI averaged RGB triplets sets of R G and B DN below a predefined threshold are discarded This threshold is typically set to 15 of maximum DN i e full sun but in some cases the level may be set lower to avoid data gaps In pilot testing using webcams a threshold of 10 was needed in some areas with very high contrast causing deep shadows in order to avoid multi day gaps in data If the 15 threshold results in a multi day gap in data for a particular camera dataset determine the appropriate threshold for that camera using this method Examine the frequency distribution of total image brightness calculated as the sum of R G and B DN in the PCIP output dataset see Figure 1 for example The distribution is typically bimodal with some very da
218. iquely identify each camera Label each camera with a sticker identifying the organization deploying the units a request not to tamper with units a contact phone number and if desired the NETN web page for phenology monitoring for people interested in more information http science nature nps gov im units netn monitor programs phenology phenology cfm Reference panels Reference panels are used for two purposes First periodic photographs of a color standard card are used to verify the camera s color balance settings and to facilitate comparisons between cameras Second a simple matte gray reference panel is included in the corner of each image in order to monitor both day to day shifts in color balance due to changes in weather conditions and to evaluate long term stability of the imaging sensor The first objective is met by taking pictures of a ColorChecker card Figure S9 2 under full sun mid day conditions Note the conditions under which the ColorChecker picture is taken are very important Standardization is most easily obtained under full sun conditions at mid day The ColorChecker card is held in front of the camera and should fill as much of the field of view as possible This is done when a camera is first deployed to provide camera specific baseline data It is done again each year at the start and end of the growing season Pictures of the ColorChecker card are considered an important part of a camera s metadata and the
219. ir Animal Checklist during a walk along a designated transect through the site NETN uses only the walk method of animal observation The standard search time will vary among sites as directed by park staff On most days monitors will observe few if any of the animal species on their list This negative data is very useful and monitors continue to record on the Animal Checklist that they did not observe the species on that date Phenophase data is only filled out for species which were observed during that visit Observers record data in a Nature s Notebook datasheet package and submit data online directly into Nature s Notebook at www nn usanpn org as described in the NETN Phenology Observer Training Manual 78 Revision History Version Date Revised by Changes Justification 1 00 July 2010 Geri Tierney 1 01 Sept 2010 Geri Tierney Adjusted procedure for one time observation Editorial changes 1 02 Oct 2010 Geri Tierney Adjusted observation definitions to match NPN change Edited text for individual plant selection 1 03 Nov 2010 Geri Tierney Logbooks will not collect personal information but will include time and comments 1 10 April 2011 Brian Mitchell Revised to match US NPN 2011 procedures Geri Tierney including abundance Dropped stationary and area search options for animal observation in favor of single walk Moved time of observation to comments for animals only Eliminated question on sit
220. is near a popular trail or visitor center However designated sites for automated monitoring may be located in a remote or hard to access area of interest Undisturbed The site should be sheltered from human disturbance Avoid sites adjacent to a building pavement farm or other human land use or areas affected by fertilizers pesticides irrigation or watering by humans or a man made heat island or other climatic disturbance Representative As much as possible sites are typical of the vegetation and climate of the target habitat Select sites which are neither excessively steep flat or dry compared to the habitat type as found in the park In forested areas select sites that are generally similar to the surrounding forest reflecting the overall canopy composition and structure Uniform Conditions should be relatively uniform across the site If species of interest are found in two adjacent but distinct habitats they are documented as separate sites For example a vernal pool occurring within a northern hardwood forest is documented as a separate site from the forest Species presence The site must contain the species to be monitored For animals the site lies within an appropriate habitat for that species and encompasses a stationary location or walking route from which the species of interest can be seen or heard Site Naming Sites are assigned names unique within the park by park staff or cooperators These are typically t
221. istration info can be collected using the Plant Registration Datasheet in Appendix A below and entered online in the same manner as site information Site and plant registration information is updated annually or if conditions change We follow the conventions of USA NPN for site and plant data collection USA NPN Technical Information Sheet July 2012 Supplementary Organismal and Site specific Information Collected via Nature s Notebook Version 1 0 http www usanpn org files shared files USA NPN_suppl_info_tech_info_sheet_v1 0 pdf If monitoring a plant as a patch it is important to report this fact when registering the plant in Nature s Notebook Click the check box for Patch to indicate it is a patch rather than a single individual and report the size of the patch 69 SOP 2 Site Selection and Set Up Revision History Version Date Revised by Changes Justification 1 00 July 2010 Geri Tierney 1 01 Sept 2010 Geri Tierney Added paragraph on informational displays Editorial changes 1 02 Oct 2010 Geri Tierney Adjusted text on individual plant selection Clarified reason for upper limit on site size 1 10 April 2011 Brian Mitchell Added section on monitored habitats and Geri Removed option for volunteer to choose Tierney custom site Adjusted number of sites per park habitat to be gt 3 and number of plants per site to be gt 3 Clarified that sites are not randomly selected Editorial changes 1 11 M
222. ite and also require some degree of user skill or previous experience in networking and photography Alternatively plant cams are less expensive than webcams and rely on batteries for power and memory cards for image storage Plant cams can be placed anywhere and operated by users with minimal training but must be visited periodically to download images and replace batteries Webcams designed primarily for indoor use did not perform adequately in pilot testing and are not used as part of this SOP Choice of specific camera model will vary depending upon budget and availability Recommended plant cams include Wingscapes PlantCam model WSCA04 no longer available for purchase as of spring 2013 and Wingscapes TimelapseCam 8 0 model WSCTO01 about 100 The TimelapseCam has higher photo resolution and more flexibility for photo scheduling than the former but no laser aiming feature Recommended outdoor webcams include models from the StarDot NetCam Axis and Vivotek product lines for these webcams cost of camera and accessories will be 500 1000 or more In particular StarDot has been responsive to designing webcams that meet the needs of scientific professionals such as by working to incorporate metadata into image files Other makes and models of cameras designed for outdoor use may be selected for use with this SOP 205 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras Camera housing and accessories Plant cams
223. k event scores findPeaks is used for both sccCor and binaryPtMatch The following example displays results from sccCor but the process is identical for both methods This function can use the cutoff value in the template or you can specify a new score cutoff To view score cutoff thresholds for a template use templateCutoff gt templateCutoff BINtemplates BTNWd1 0BIN BTNWpoint1 OBIN BTNWd 8BIN BTNWauto 5BIN 9 9 9 9 To specify new score cutoff thresholds for a template use templateCutoff again gt templateCutoff BINtemplates lt c 9 10 10 13 10 12 14 The only required argument for findPeaks is score obj the output from sccCor As usual assign the output to an object in R gt CORpks lt findPeaks score obj scc parallel FALS Gl 170 SOP 8 Automated Sound Detection and Classification Done with BTNWd1 0 Done with BINWpartial Done with BTNWd 8 Done with BTNWd 5 Done with BTNWd 2 Done with BTNWauto 8 Done with BTNWauto 2 Done The output is an object of class foundPeaks which contains a list of lists for each template The first list for each template contains a data frame of all correlation peaks pks the second list contains a data frame of peaks greater than the specified cutoff hits and the third is a one line summary of the first two A summary of the results can be viewed by typing in the name of the object they were assigned to gt CORpks A foundPeaks object 7 tem
224. ke sleep without losing its place in the schedule Change the memory card and batteries while the unit is sleeping and then follow the procedures on the previous page for installing the SD cards and verifying the schedule and settings The desiccant packet is checked regularly and replaced with a fresh packet anytime it appears swollen Remember to fill out the Deployment Datasheet completely Downloading Audio Data from Olympus and Song Meter ARUs SD Cards Both the Song Meter and Olympus recording units with an SD adapter store the audio data they record on standard sized SD Secure Digital cards SDHC that can be purchased online or at most electronics stores The Olympus recorder can also use a micro SD card SD card are available in sizes up to 32 GB and micro SD cards are available in sizes up to 16 GB The Olympus recorder uses a single card the Song Meter SM1 can use one or two cards and the SM2 can use up to four cards The choice of memory capacity will depend on the project budget recording sample rate and schedule and expected maintenance schedule In general it helps to purchase the largest capacity cards that the project budget can afford The price for a 16 GB SD card is around 25 currently while the price for a 32 GB card is around 50 currently micro SD cards are more expensive Prices are expected to drop in the future following the trend of data storage becoming cheaper over time Download Once collected fr
225. l 5 after making one selection at a density of 0 2 Call 6 specify tighter time and frequency limits use automatic selection BTNW_auto_d100_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav t lim c 0 5 2 5 frgq lim c 3 5 6 75 128 SOP 7 Acoustic Template Creation select auto Call 7 automatic selection at density 0 8 BTNW_auto_d80_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav t lim c 0 5 2 5 frq lim c 3 5 6 75 select auto dens 0 8 Call 8 automatic selection at density 0 2 BTNW_auto_d20_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav t lim c 0 5 2 5 rq 17mM 6 3 5 6 75 7 select auto dens 0 2 20 40 60 80 20 40 60 80 Frequency kHz Time s Frequency kHz SR PR ewe Pewee me he et ee Time s Figure S7 3 Automatic selection at different densities Top left call 6 at density of 1 0 Top left call 7 at a density of 0 8 Bottom call 8 at density of 0 2 Call 9 line selection BTNW_line_d100_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav select line Call 10 line selection at density 0 5 BTNWlineO 5_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav select line dens 0 5 Call 11 point selection BINW_click_allNotes_C lt makeCorTemplate clip C Users jkatz3 Dropbox L
226. l degrees WGS84 Record to four decimal places eg 42 4910 Elevation feet above sea level from a GIS layer or topo map Development The degree of development surrounding the site can best be described as e Suburban Sites surrounded mostly by houses with yards Rural Surrounded by farms or mowed or grazed pastures or near a rural residence or ranchette Wildlands or semi wildlands Within natural habitats managed woodlands or grazed rangelands Other describe in comments Habitat type Record the habitat as Landscaped area eg garden lawn Shrubland shrub thicket or shrubby field Agricultural field cropland or pasture Forest or woodland Orchard or tree farm Open wetland eg marsh or bog Grassland or meadow Forested wetland such as swamp Beach dune salt flat or barren land Other describe in comments Distance to Road feet yards miles circle unit of measure Estimate the distance in feet yards or miles from the center of your site to the nearest road Distance to Permanent Body of Water feet yards miles circle unit of measure Estimate the distance from the center of your site to the edge of the nearest permanent body of water Site area acres square feet square yards circle unit of measure Record the approximate area of the site in acres square feet or square yards Site Comments Please include any useful informati
227. l frequency response During recording or playback mode Linear PCM format Overall frequency Recording mode response 48 kHz 40 Hz to 23 kHz 44 1 kHz 40 Hz to 21 kHz MP3 format Overall frequency Recording mode response 320 kbps 40 Hz to 20 kHz 256 kbps 40 Hz to 20 kHz 192 kbps 40 Hz to 19 kHz Maximum recording time per file 128 kbps 40 Hzto 17 kHz Linear PCM format E WMA format WMA format 48 kHz 3h STXQ 26h 40min Recording mode Oxeral scquency 44 1 kHz 3h 20min STHQ 26h40min MP3 f STSP 53h 40min STXQ 40 Hz to 19 kHz MP3 format HQ 26h 40min STHQ 40 Hz to 16 kHz 320kbps 29h 40min SP 53h 40min STSP 40 Hz to 9 kHz 256kbps 37h10min 7 LP 148h 40min HQ 40 Hz to 13 kHz 192kbps 49h 40min SP 40 Hz to 8 kHz 128kbps 74h 30min LP 40 Hz to 3 kHz 89 SOP 5 Building an Autonomous Recording Unit Maximum Recording Times Based on Storage Media Linear PCM Format Recording Mode 8GB micro SD Card 16GB micro SD Card 32GB micro SD Card 48 kHz 11h 22h 44h 44 1 kHz 12h 24h 36 h MP3 Format Recording Mode 8GB micro SD Card 16GB micro SD Card 32GB micro SD Card 320 kbps 54h 108 h 216h 256 kbps 68 h 132 h 264 h 192 kbps 90 h 180 h 360 h 128 kbps 136 h 272 h 544 h WMA Format Recording Mode 8GB m
228. lassification Appendix S8 A Creating a MySQL database continued Databases B SQL amp Status Users 4 Export Import P Settings iB Synchronize Replication gt Variables Charsets More Run SQL query queries on server localhost SET OLD_UNIQUE_CHECKS UNIQUE CHECKS UNIQUE _CHECKS 0 2 SET OLD_ FOREIGN KEY CHECKS FOREIGN KEY CHECKS FOREIGN _KEY_CHECKS 0 SET OLD SQL MODE SQL MODE SQL MODE TRADITIONAL ALLOW_INVALID DATES a CREATE SCHEMA IF NOT EXISTS Acoustics DEFAULT CHARACTER SET latinl COLLATE latinl_ swedish ci USE Acoustics Table Acoustics tblPerson DROP TABLE IF EXISTS Acoustics tblPerson CREATE TABLE IF NOT EXISTS Acoustics tblPerson pkPersonID INT NOT NULL AUTO_INCREMENT COMMENT The unique ID assigned to each person Thic numhar ic antamaticsallw saccianned ta aarh narenn sand tha fiald carwoaoc ac tha nrimarr Gear Delimiter Show this query here again _ Retain query box a To make sure the code executes successfully click on the acoustics database in the left menu You should see all of the tables listed You can select a table and Browse it to see the data the tables should be empty at first You can also select Structure to see the column names p h p MyAdmin CTinstance29243 db xeround com 19055 acoustics oa e Y Structure j SQL Search Query Export lt Import
229. last seedling to emerge in the spring are avoided since they may not be representative of the larger population at a site If a plant grows in a large mass where it is difficult to distinguish or mark individuals staff may choose to designate the plant as a patch If monitoring as a patch it is important to correctly mark and register the patch as described below It is important that plants are correctly identified to species before data is submitted Species recommended for monitoring by this protocol are readily identifiable to species using information provided during training or in field guides Program staff should verify correct identification of all marked individual plants Select Walking Route It is impractical for volunteers to mark and monitor individual animals so animal species are monitored as a population at each site Animals are observed along a marked walking route through each site Program staff or cooperators select and mark a single route through each site This route should encompass areas where the animal species of interest have been seen or heard but should avoid disturbance to nesting sites or sensitive areas Marking Marking is used to uniquely identify and delineate each site walking route and monitored plant Specific marking conventions are determined by park staff at each participating park in keeping with aesthetic standards for the park If allowed by park staff individual plants may be selected and marked
230. le fldSpeciesCode VARCHAR 10 NULL COMMENT The four six eight or ten letter code which identifies a particular species PRIMARY KEY pkSpeciesID ENGINE InnoDB COMMENT Store species info Use BBL codes or other 4 6 or 8 chara comment truncated Table acoustics tblTemplate DROP TABLE IF EXISTS acoustics tblTemplate CREATE TABLE IF NOT EXISTS acoustics tblTemplate pkTemplateID INT NOT NULL AUTO_INCREMENT fkSpeciesID INT NOT NULL PersonID INT NULL LocationID INT NULL ldTemplateName VARCHAR 96 NULL COMMENT Name should refer to the ies code and allow for multiple templates per species ldRecordingDate INT NULL COMMENT Date template sound clip was recorded x spe Wo HG FQ FFF fldRecordingEquipment gt VARCHAR 100 NULL COMMENT Make amp model of recorder and microphone fldClipPath VARCHAR 255 NULL COMMENT Full file path to clip ldSampRate INT NULL COMMENT Sample rate of clip ldPtOn LONGTEXT NULL COMMENT On points binary templates yet ldPtOff LONGTEXT NULL COMMENT Off points binaryPtMatch only mh Fh Fh onl mk 7 ldPts LONGTEXT NULL COMMENT All points correlation templates only ldTStep DECIMAL 16 16 NULL COMMENT Size of time steps ldFrqStep DEC
231. lected adjacent to on points If the buffer is greater than 0 off points can only approach on points to the edge of the buffer The binary aspect of the template building process allows you to view the song clip as either signal or noise and the user can specify the threshold that separates the two If you already know what amplitude threshold to use for the binary spectrogram you can set that in the call or leave it out to adjust it in the next step A new window will open to display the spectrogram of the chosen clip Time is labeled along the X axis and frequency is labeled along the Y axis The spectrogram is a matrix of time and frequency bins and the corresponding bin numbers are labeled along the secondary X and Y axes If binary FALSE the spectrogram will be displayed in the assigned color palette If binary TRUE the spectrogram will be black and white If the amplitude cutoff was not set in the function call you will be prompted to raise or lower the threshold by typing h or I higher or lower and pressing Enter You can adjust it in broader steps by typing in more than one character hhh raises the threshold more than h Enter h Enter h Enter and you can enter as many as five characters at once When only the signal remains black and the noise is white press Enter once more to begin point selection If the selection method is set to click you will be prompted to select individual points to inc
232. les directly to the survey folder returns the same metadata as fileCopyRename does for wav files and renames the new surveys according to their location prefix and the time and date they occurred There is no file type conversion between copying the survey files and scanning them with the detector functions Function mp3Subsamp relies on third party software to split the mp3 files without decoding and re encoding them Before using this function the zip file or the installer must be downloaded from http mp3splt sourceforge net mp3splt_page home php Note that no administrator permissions are required to install from the zip file To use mp3Subsamp a survey duration in seconds must be specified as well as the number of minutes between surveys the directory where the recordings currently are and the directory where they should be saved to when extracted The function also requires the bitrate of the The Olympus model NETN typically uses does not have a wav option but some Olympus models do 163 SOP 8 Automated Sound Detection and Classification recording the sample rate and the number of channels to be specified in the call The default settings of 600 seconds ten minutes from the top of every hour recorded at 128 kbps in stereo at 44100 Hz match the setup described in SOP 6 surveydata lt mp3Subsamp from C Users jkatz3 Dropbox UVMacoustics Analysis Recordings to C Users jkatz3 Desktop TestFolder
233. lfway through the interval prior to recorded date as described below Any event date occurring directly after an interval exceeding 7 days in length is discarded from the dataset When multiple observers are reporting for the same individual use the first date reported by any trained observer considered as typical or expert and use observations from all observers to calculate the prior interval Phenophase start date For each individual plant or animal species monitored at a site estimate phenophase start date as the first date recorded as yes minus the days within the prior interval divided by two and then rounded down to the last whole number Prior interval refers to the interval between the previous visit and the visit first recording yes Estimate error as the prior interval divided by 2 For example if yes recorded on day 8 was preceded by no recorded on day 7 the start date is day 8 0 5 days if yes recorded on day 8 was preceded by no recorded on day 6 the start date is day 7 1 day and if yes recorded on day 8 was preceded by no recorded on day 5 the start date is day 7 1 5 days Phenophase underway This event may be a better indicator of ecological impact than start date and may be less subject to bias For each individual plant monitored at a site estimate phenophase underway as the first date that abundance is recorded in the second abundance category typically the 5 24 or
234. lly coherent fingerprint of climate change impacts across natural systems Nature 421 6918 37 42 Richardson A D B H Braswell D Y Hollinger J P Jenkins and S V Ollinger 2009 Near surface remote sensing of spatial and temporal variation in canopy phenology Ecological Applications 19 6 1417 1428 Root T L J T Price K R Hall S H Schneider C Rosenzweig and J A Pounds 2003 Fingerprints of global warming on wild animals and plants Nature 421 6918 57 60 Schwartz M D editor 2003 Phenology An Integrative Environmental Science Kluwer Academic Publishers Dordrecht Sparks T H and P D Carey 1995 The responses of species to climate over two centuries An analysis of the Marsham phenological record 1736 1947 Journal of Ecology 83 321 329 Sparks T H F Bairlein J G Bojarinova O Hiippop E A Leihikoinen K Rainio L V Sokolov and D Walker 2005 Examining the total arrival distribution of migratory birds Global Change Biology 11 22 30 Tryjanowski P S Kuzniak and T H Sparks 2005 What affects the magnitude of change in first arrival dates of migrant birds Journal of Ornithology 146 200 205 Thomas K A E G Denny A J Miller Rushing T M Crimmins and J F Weltzin 2010 The National Phenology Monitoring System v0 1 USA NPN Technical Series 2010 001 van Strien A W Plantenga L Soldaat C van Swaay and M Wallis deVries 2008 Bias in phenology assessments based
235. lothing only not for use on skin e Permethrin kills ticks that come in contact with treated clothing and one application lasts two weeks or more Do not treat the clothing more than once every two weeks e Carefully read and follow manufacturer s instructions for application and refer to the MSDS sheet if you have questions e Do not apply while clothing is being worn e Apply to clothing item in a well ventilated outdoor area protected from wind e Lightly moisten the fabric with permethrin do not saturate the fabric e Allow clothing item to dry outdoors for at least two hours before wearing 4 hours in humid conditions e Keep treated clothes in a separate bag for storage and transport e Launder treated clothing separately from other clothing More information on permethrin http www epa gov oppsrrd1 REDs factsheets permethrin_fs htm http drugsafetysite com permethrin Prophylactic preventative use of antibiotics Antibiotics are sometimes used to prevent Lyme disease transmission from the deer tick Antibiotics may be prescribed following a deer tick bite if the tick was attached for 24 or more hours AND the bite occurred in an area where Lyme disease is common Other tick borne diseases are usually treated using antibiotics only after symptoms become obvious A few things to keep in mind about antibiotic therapy According to the US Public Health Service Centers for Disease Control e Every time a per
236. lude as on and off points in the template Do this by hovering your mouse over the points you gt Fast Fourier Transformation 133 SOP 7 Acoustic Template Creation intend to select and left clicking each point Right click to end the on point selection process and the R gui will prompt you to choose off points Do this by hovering your mouse over the points you intend to select and left clicking each point Right click to end the off point selection process Close the spectrogram window If the selection method is set to rect or rectangle you will be prompted to select the upper left corner of a rectangle in which all signal points will be selected as on points Do this by hovering your mouse over the spectrogram where you want the upper left corner to be and left clicking left click and release You will then be prompted to choose the lower right corner of the rectangle Again move your mouse and left click to select the corner All on points within the rectangle will fill with a transparent color if the function call included the default dens 1 the on points will be a solid orange If dens was set to less than 1 the on points will be dotted orange at roughly the density specified You can select multiple rectangles per template to incorporate some areas while leaving out others Right click to end the on point selection process You will now be prompted to select the upper left corner of a rectangle in which all noise point
237. luding Nature s Notebook Nature s Notebook www nn usanpn org is the online plant and animal phenology observation program of USA NPN We wish to acknowledge the important contributions to this protocol made by M Albert who helped implement the pilot project and by J Gross P Nagler and S Gage who contributed useful reviews which improved this document Also we acknowledge and appreciate collaborative discussions with staff of the California Phenology Project CPP This project was funded in part by a grant from the USGS National Park Monitoring Project Any use of trade product or firm names is for descriptive purposes only and does not imply endorsement by the U S Government List of Terms and Acronyms ACAD Acadia National Park APPA Appalachian National Scenic Trail ARU Autonomous recording unit BOHA Boston Harbor Islands National Recreation Area I amp M National Park Service Inventory and Monitoring Program MABI Marsh Billings Rockefeller National Historical Park MIMA Minute Man National Historical Park MORR Morristown National Historical Park NETN Northeast Temperate Network NHP National Historical Park NHS National Historic Site NPS National Park Service NST National Scenic Trail PRA Paperwork Reduction Act of 1995 ROVA Roosevelt Vanderbilt National Historic Sites SAGA Saint Gaudens National Historic Site SAIR Saugus Iron Works National Historic Site SARA Saratog
238. lug connector and waterproof the RCA connections Final Assembly Slide the plastic plate down the microphone wire until it stops on the cable tie Push the wire tails of the windscreen shell holder through the holes in the plate and bend them down with pliers Slide the windscreen shell onto the holder it should fit snugly and stay in place without additional fasteners Drill a hole in the back of the Pelican case behind where the 2x2 will rest Place the lauan back board into the Pelican case behind the audio connector and fix the back board in place by screwing from the back of the Pelican case into the 2x2 board with the deck screw Tighten the screw so that it seals against the plastic Pelican case Plug the audio connector into the top of the recording unit Strap the recoding unit to the 2x2 board with the Velcro straps Plug the microphone into the female phone plug on the outside of the Pelican case and power on the recorder Test the microphone for function If multiple recorders are deployed it may be worth testing all microphones in a controlled manner to verify that all are similarly sensitive If the recorders will be deployed in areas with traffic use one or two locks with at least a 3 4 shackle to secure the door closed Observe that the recorder will function with only two batteries installed if they are installed side by side within the same battery holder Using only two batteries will reduce the run time by 50 In the p
239. ly attached to each file The NETN Phenology Monitoring Protocol provides detailed instructions for training of monitors making repeated observations site selection and setup deployment and maintenance of audio recorders data collection quality assurance quality control and data stewardship For data collection by observers this protocol utilizes datasheets phenophase descriptions and other materials developed by USA NPN These materials have been carefully designed to clearly and specifically describe phenophases and associated data collection for observers from diverse 223 SOP 11 Data Management and Quality Assurance Quality Control backgrounds USA NPN 2011 USA NPN has incorporated many QA QC measures into their procedures and their Nature s Notebook online interface Online QA QC measures include the use of carefully designed and tested menus utilizing pick lists to reduce data entry errors During training all monitors making repeated observations receive explicit instructions describing how to make and report phenological observations on the species selected for observation in that park They are also given information describing the sites at which observation occurs within that park Park level coordinators provide another level of quality assurance These coordinators select and mark sites for observation and select or oversee selection of individual plants to be monitored Thus species identification errors for plants ar
240. m Manager continually solicits feedback from the contractor and NPS staff on safe execution of the protocol including risk control options not considered thus far 54 SOP 1 Safety Appendix 1 B Job Safety Analysis JOB TITLE Phenology Monitor Xx NEW JOB SAFETY ANALYSIS Phenology Monitoring Field Work and DEPARTMENT LI REVISED Travel to from and within Parks Northeast Temperate Network LI REVIEWED ANALYSIS BY John Karish NER I amp M Brian R Mitchell NETN Program Program Manager Manager Required and or Recommended Personal Protective Equipment Required At least one method of communication i e cell phone in most parks Personal Locator Beacon and SPOT GPS Messenger at ACAD driver s license Recommended as appropriate first aid kit rain gear condition appropriate footwear and clothing sufficient food and water Potential Hazards Recommended Action or Procedure Planning and Not being prepared and following Plan ahead Know where you will be going the Communication plan itinerary route to be surveyed and any particular hazards Communication breakdowns associated with the monitoring route Check the weather forecast and plan accordingly For visits to remote or hard to access locations check in with park resource manager or designated individual RM DI prior to field work with a trip plan and after field work to confirm the work is safely completed Contact the RM DI with any changes including
241. m automatic recorders are stored by the NETN data manager until those files can be submitted to the National Phenology Database via Nature s Notebook Responsibility for data management is shared between park coordinators and the NETN Data Manager as described in the Data Management and Quality Assurance Quality Control SOP Quality Assurance Quality Control To ensure the quality of monitoring data collected in this program we rely on standardized written protocols and datasheets careful training for monitors making repeated observations and oversight by park level coordinators For digital data collection we employ standardized file naming procedures and data imprinting on imagery for assurance that site and date metadata are correctly attached to each file Quality assurance and quality control QA QC methods are described in the Data Management and Quality Assurance Quality Control SOP Data validation is made by comparing phenological data from multiple methods at the same site and at related sites i e similar sites at the same park Data collected by untrained and trained volunteers and from automated cameras and audio recorders will be compared to identify possible bias introduced by method by training or lack or training by frequency of collection and by species or phenophase observed Data Analysis Integration and Reporting Network staff obtain data from USA NPN at regular intervals but no less often than annually Analy
242. me between maintenance visits for high frequency bat monitoring a and mixed bat and bird monitoring b 105 SOP 6 Deployment and Maintenance of Autonomous Recording Units Installation Supplies and Equipment Song Meter recording units with SD cards and microphones SM2PWR cable wildlifeacoustics com or equivalent if using external power 4 6 Plastic 14 cable ties cabletiesplus com item CP 14 120 B Group 24 12V deep cycle battery or 4 D cell batteries buy locally Group 24 12V battery case if using external batteries amazon com item B00100D6QA 5 4 and 7 Diameter hose clamps to secure lid of battery box 4 3 32 vinyl coated steel cable and a 1 8 cable clamp 8 3 32 cable with swaged loops at ends for securing battery box to a tree 2 Packets of silica desiccant Knife diagonal pliers to trim cable ties Phillips 2 head screwdriver to open and close unit 5 16 socket or nut driver Items listed above with no specified source can be sought at your local hardware store Procedure Select a location with a tree or post that is between around 10 cm 4 and 30 cm 12 in diameter If possible avoid placing the unit where it will be in direct sunlight during the hottest part of the day early afternoon in summer If using external power an ideal tree has an area at the base suitable to place a 12v deep cycle battery in a box The battery should not tip over and should not be immersed in water if heavy ra
243. ment laboratory s acoustic library An archive for studying soundscape ecology Ecological Informatics 12 50 67 Lieth H 1974 Purposes of a phenology book in H Lieth editor Phenology and Seasonality Modeling Springer Verlag New York Miller Rushing A J T T Hoye D W Inouye and E Post 2010 The effects of phenological mismatches on demography Philosophical Transactions of the Royal Society B 365 1555 3177 3186 Miller Rushing A J D W Inouye and R B Primack 2008a How well do first flowering dates measure plant responses to climate change The effects of population size and sampling frequency Journal of Ecology 96 1289 1296 25 Miller Rushing A J T L Lloyd Evans R B Primack and P Satzinger 2008b Bird migration times climate change and changing population sizes Global Change Biology 14 1959 1972 Mitchell B R W G Shriver R Dieffenbach et al 2006 Northeast Temperate Network Vital Signs Monitoring Plan Woodstock VT National Park Service Technical Report NPS NER NRTR 2006 059 http science nature nps gov im units NETN monitor monitor cfm Moussus J P R Julliard and F Jiguet 2010 Featuring 10 phenological estimators using simulated data Methods in Ecology and Evolution 1 140 150 Parmesan C 2006 Ecological and evolutionary responses to recent climate change Annual Review of Ecology Evolution and Systematics 37 637 669 Parmesan C and G Yohe 2003 A globa
244. minant species of vegetation in that region It is important the ROI be large enough that any minor shifts in the field of view over time will not substantially alter the delineated region For example the ROI should fall within an area bordered by enough foliage that a minor shift in field of view will not shift the ROI off the foliage 217 SOP 10 Processing Image Data ROIs are selected and saved using the analysis software program as described in the document Installing and Using PhenoCam It is very important to save the ROI from each analysis so that they may be used to designate the same region when analyzing images from this site in subsequent years Calculating gcc Long term datasets of repeat images taken hourly for several months or several years show scene illumination changes due to the daily rotation of the Earth the Earth s revolution cloudiness and other changes in overall weather conditions This variation is unrelated to the variable of interest canopy greenness To suppress the influence of these scene illumination changes on time series of canopy greenness we follow the procedure recommended by Sonnentag et al 2012 and calculate green chromatic coordinate as gcc G R G B where R G and B represent respectively red green and blue digital number DN We use PCIP to extract RGB DN within the region s of interest As a quality check at sites where vegetation canopies are monitored we select an addit
245. monitors so that Nature s Notebook can be open on one screen for data entry and photos can be viewed on another The basic procedure written for Windows XP is as follows e Photos should be organized so that all photos for a given individual and year are in the same folder see SOP 11 Data Management and QA QC for file name conventions e Open an instance of Windows Explorer on one screen and maximize the application Navigate to the folder with the correct individual and year and change the View setting to Filmstrip View Filmstrip in Windows XP Shrink the size of the file navigation pane if needed to enlarge the photo so plant phenology can be easily viewed 220 SOP 10 Processing Image Data e Open an instance of Nature s Notebook on the other screen log in and open a data entry form for the individual Alternatively print out a data form and record data on the form then follow up with entry on line e Starting with the earliest photo the left most photo if the photos have been named properly evaluate one photo per day for phenology and record the data in Nature s Notebook o Make sure to use the correct individual or portion of individual or patch of individuals the focal area for recording data and never change the focal area over the course of a season of data without noting this in Nature s Notebook some changes will require setting up a new individual or patch in Nature s Notebook
246. mperate corresponding to the site of deployment Network Prepare Units Please Do Not Disturb Camouflage the units using brown and green spray paint before deployment to reduce the visibility of the equipment Additionally For information call each unit must have a unique identification number permanently 555 656 3011 assigned and engraved or otherwise permanently affixed to it We use the Olympus recorder serial number as this ID number to assist with documenting potential equipment problems and facilitate deploying units at the same site each 95 SOP 6 Deployment and Maintenance of Autonomous Recording Units year Each unit is also labeled with a sticker identifying the organization deploying the units and a request not to tamper with units See example at right with dummy contact number The contact phone number is the NETN Program Manager s number 802 457 3368 x37 for network units or the Park Coordinator s number for park owned units It may also help to include the NETN web page for phenology monitoring for people interested in more information http science nature nps gov im units netn monitor programs phenology phenology cfm Test the Unit A few weeks before taking the unit into the field insert a memory card and make a test recording Download the recording and verify that the unit is working as it should and is not recording distorted files or files full of static This is especially important if a unit ha
247. n the number of parks participating as well as the number of volunteer observers recruited to observe at each park The following is a plausible workload scenario based on moderate participation at most NETN parks However as the program develops this workload scenario should be updated to reflect actual time spent Project leader 0 17 Full Time Equivalent FTE or 8 weeks This includes time participating in pre season preparation and park coordination as well as annual data analysis and reporting Park coordinator 0 05 FTE or 2 weeks This includes recruiting and providing logistical support to volunteers and identifying and marking monitoring sites walking routes and individual plants NETN Data Manager 0 05 FTE or 2 weeks This includes obtaining and archiving NETN park phenological data from the USA NPN database and participating in the annual operational review NETN Science Communication Specialist 0 07 FTE or 3 weeks This includes updating annual training materials and providing trainings at participating parks during annual park visits Park Volunteers 1 2 hours per week during season of observation potentially March to November This includes time spent traveling to observation sites observing and submitting data online into Nature s Notebook The following is a rough schedule of events for annual monitoring activities January Completion of prior year data analysis and reporting Discussion
248. ncy data are discarded if they occur simultaneously with high amplitude frequencies MP3 files save considerable storage space versus uncompressed files but obligatory decompression time can be substantial Spectrogram cross correlation A method for seeking a known template in a survey consisting of unknown songs The correlation of amplitude values in the FFT template matrix to a matrix in the survey is measured using the Pearson method The survey matrix then shifts one time bin and the correlation to the template is measured again The user specifies a minimum Pearson score and local maximum scores identify events Survey A recording that will be searched for the template Must be a WAV or MP3 file and must be longer than the template Template A recorded song example which will provide the search image for the computer Must be a WAV or MP3 file A template may differ from a simple song clip by retaining bandpass filter values and score cutoff values WAC The Wildlife Acoustics proprietary compression format Use of this format is restricted to Wildlife Acoustic s Song Meter recording units These units are the data collection standard due to their flexible timed recording high storage capacity ultrasonic recording options data logging and GPS integration and weatherproofing WAC files must be converted to WAV files for use in the R environment using Wildlife Acoustics conversion software WAV An uncompressed linear PCM audio f
249. ne segment behind each battery holder so that it can loop around the front to secure the batteries in place Use two screws in each holder to fasten each battery holder to the lauan back plate allowing a 4 margin between the edge of the holders and the edge of the 2x2 that is already screwed to the back plate Use the wire cutters to trim the leads so they are the same length and use the wire strippers to remove of insulation Twist the two red leads together Twist the two black leads together Strip 4 from the two lengths of 18 gauge wire and solder them to the respective colored leads If using shrink fit tubing to insulate connections slip a 1 25 length onto each lead covering the junction and heat it with the soldering iron to shrink it Strip Y of insulation from the free end of the extended leads twist the stranded wire of each lead into a coherent element and make a 90 degree bend in the exposed wires Solder the red lead to the brass screw by placing the 90 degree bend immediately below the head of the screw Solder the black wire to the brass tack in the same fashion Cut the dowel into two 1 5 8 pieces to match the size of a AAA battery In the center of one end of a dowel piece insert the brass screw by holding the screw steady with a screwdriver and twisting the dowel in In the center of an end of the other dowel push in the brass tack Insert the dowels into the 84 Be sure to properly align
250. nits These units are the data collection standard due to their flexible timed recording high storage capacity ultrasonic recording options data logging and GPS integration and weatherproofing WAC files must be converted to WAV files for use in the R environment using Wildlife Acoustics conversion software WAV An uncompressed linear PCM audio file format owned by Microsoft that is in widespread use sufficient to be considered cross platform As a result WAV files are playable on nearly all devices 159 SOP 8 Automated Sound Detection and Classification Data Management This protocol outlines two methods of data management Local data management relies on the analyst to name and file comma separated values csv input and output documents while MySQL database management automates this process in a relational database There are several advantages to the MySQL database including 1 reduction in file management errors 2 ability to have multiple users access the same database and 3 reduction in analyst time dedicated to data organization tasks Setup time should be minimal as a database schema is attached to this document in Appendix S8 B NETN plans to use a database implementation rather than local data management Contact the NETN database manager for access to the database A relational database consists of a set of tables that relate or link to each other Several naming conventions help distinguish tables in the database from th
251. nological data on alpine and forest wildflowers in the White Mountains of New Hampshire and Maine for several years and has recently added a group of southern New England and mid Atlantic wildflowers to their phenology program The AMC project is a good example of how to successfully engage a hiker community Project BudBurst www budburst org and Journey North http www learner org jnorth are well known nationwide programs which encourage citizens and students to observe and report phenological observations on plants and animals respectively Other nation wide programs such as eBird encourage volunteers to observe and submit repeat monitoring observations and thus provide phenological data even though phenology may not be a specific program goal In addition to these programs there is a long history of scientists and amateurs recording phenological observations in the United States and elsewhere in the world Schwartz 2003 These programs and historical studies used a variety of methods for monitoring phenology The USA NPN seeks to create partnerships and data sharing among organizations interested in phenology and has developed monitoring standards to facilitate the integration of data from ongoing programs historical data sets and newly collected data Denny et al submitted By partnering with USA NPN we facilitate integration of NETN data with other contemporary and historical datasets Pilot Project The NETN parks and network off
252. nology We focus network wide efforts on a short list of selected species in order to provide sufficient data to determine trends Fifteen plant and 12 animal species occurring within two core habitats Northern hardwood forest and Vernal pools and five optional park habitats have been selected for phenology monitoring To accomplish these objectives NETN uses three approaches 1 park visitors are recruited on site to submit one time phenological observations at marked locations 2 interested volunteers and park staff are recruited and trained to submit repeat phenological observations and 3 automated sensors digital cameras and audio recorders are used to record data at select locations In addition to collecting data at an optimal frequency automated sensors can be used at difficult to access or sensitive sites or can provide a useful quality assurance check when used ix in conjunction with volunteer observations Detailed standard operating procedures SOPs included in this protocol provide step by step instructions for monitoring using each approach Pilot testing of our methods began in 2009 and continued through 2012 We monitor phenological status and intensity or abundance using phenophases defined by USA NPN Appendix A rather than the more traditional phenological event A phenophase is a specific seasonal life history stage or behavior such as a plant having open flowers or a bird singing This status based approach is da
253. nt Record for unknown M for male F for female or Both Comments Record any additional features that seem important such as anything that makes this plant unusual 72 SOP 3 Observer Recruitment and Training Northeast Temperate Network Version 1 11 Overview This SOP describes practices for recruiting training and supporting observers for the NETN Phenology Monitoring Program This program operates with both staff and volunteer observers NETN has developed and maintains a Phenology Observer Training Manual which is an accessory document to this protocol and can be obtained online at the NETN website http science nature nps gov im units netn monitor programs phenology phenology cfm or from NETN staff This SOP will be updated annually to improve training and support procedures and to incorporate useful suggestions by observers and coordinators Recruiting volunteers Phenology monitoring is interesting and methods are straightforward making it suitable for participation by volunteer observers Many opportunities exist for recruiting volunteers to participate in this program Park coordinators may recruit volunteer observers using these methods e Invitations to existing volunteers and trail club members Announcements at NPS and park related events Trail days etc Postings in local media Postings using social media Facebook Twitter etc Solicitations on associated websites ATC AMC USA NPN N
254. nts when hiking Wear clothes including pants and long sleeved shirts that are light colored and check for ticks on clothing after traveling through vegetation Conduct a thorough tick check every evening after completing field work Know how to identify tick life forms and the signs amp symptoms of tick borne diseases 57 SOP 1 Safety Appendix S1 B Job Safety Analysis continued Potential Hazards Recommended Action or Procedure Venomous snakes Being bitten by a venomous snake Venomous snakes are rare in NETN parks although more common along southern portions of the Appalachian Trail Be alert for snakes in thick vegetation and rocky habitats Look before putting hands or feet in places out of immediate view Treat all bites as if envenomation has occurred Immobilize the bitten area and keep it lower than the heart Apply a bandage wrapped two to four inches above the bite to help slow the venom This should not cut off the flow of blood from a vein or artery the band should be loose enough to slip a finger under it Remove rings watches shoes etc before swelling begins in earnest Seek medical attention immediately and or call for help Remain calm Rattlesnake bites are more likely to be life threatening Walking through Cut scratched or bruised by Shield your eyes and face with your hands thick vegetation vegetation eye or ear injuries glasses or hat when moving through tall thick brush
255. oes this camera use 213 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras Appendix S9 B Sample Plant cam Maintenance Datasheet Equipment Writing utensil Empty SD cards Charged batteries Date Location Park Site Lat Long Empty Taken Out Full Put In Unit SD Card SD Card Battery Battery Notes Plant cam checklist ____ Replace batteries ____ Replace SD cards ____ Record SD card and battery numbers in datasheet ____ Check the unit and cables over for any damage or needed adjustments ____ Remember to shut all units and battery cases 215 SOP 10 Processing Image Data Northeast Temperate Network Version 1 03 Overview Digital timelapse photography can be an important data source for long term phenological research providing a consistent and objective stream of data at optimal frequency in both accessible and remote locations This SOP provides specific procedures for processing digital image files to track seasonal development of individual plants and vegetation canopies Red green blue RGB color channel information is extracted and transformed to green chromatic coordinate gcc as an indicator of canopy greenness which is tracked over time This analysis is performed on image datasets collected from outdoor netcams and plantcams maintained by NETN as well as on image datasets collected from various cameras by volunteers at NETN de
256. of individual plants and vegetation canopies Park coordinators choose to use either outdoor webcams cameras directly addressable via Internet Protocol or plant cams inexpensive outdoor time lapse cameras targeted at hobbyists Park coordinators may process raw image files either by using specialized software PhenoCam Image Processor or PCIP to extract an indicator of canopy greenness or by manually extracting flowering and other phenophase information by viewing image datasets from individual plants To ensure the quality of monitoring data collected in this program we rely on standardized written protocols and datasheets careful training for monitors making repeated observations and oversight by park level coordinators For digital data collection we employ standardized file naming procedures and data imprinting on imagery for assurance that site and date metadata are correctly attached to each file Data validation is made by comparing phenological data from multiple methods at the same site and at related sites i e similar sites at the same park All computer data files are stored in duplicate to guard against data loss from hard drive failure Responsibility for data management is shared between park coordinators and the NETN Data Manager as described in the Data Management and Quality Assurance Quality Control SOP Network staff include phenology reporting within annual Weather and Climate Reports for parks participating in thi
257. ol is useful because it allows various unique song types to reach peak correlation with another song at slightly different times In this example by setting tol 2 0 I am willing to call peaks within two seconds of one another as correlations with the same song The output of compareTemplates is a list of four easy to compare matrices gt names comp 1 times mean times times mmss scores The matrix times has units decimal seconds identical to the matrix times mmss which has units mm ss ss The matrix scores is the one we are most interested in since it will allow us to compare the score of all the templates View all matrices at once 150 SOP 7 Acoustic Template Creation Comp or view just the matrix of scores compS scores For larger matrices it might be better to save them for viewing in Microsoft Excel write csv compSscores E users jkatz3 Desktop SOSPtemplates tmpltComp csv Opening this file in Excel you can see the matrix with the template names in the column headings and the average peak time in the row names Because the survey file is a list of all of the example song clips in the same order the diagonal should be the correlation of each song against itself which would be 1 00 except in cases where the bandpass filter removes some low or high interference Each column of this table represents the result of a single template so the most logical way to read this table is down the columns rather
258. om the field the audio files on SD cards are downloaded onto an office computer or external hard drive using a USB based SD card reader The card is plugged into the reader and the reader is then plugged into the USB port of a computer and the device should then appear on the computer Files can then be moved to the location directed by your data management plan The date a given audio file was recorded should be shown in the properties of the file under date modified but keep in mind that if any manipulation is done to the file this information may be lost If this unit has been properly set up to assign the correct four digit prefix for the file names they will appear for the Olympus ARU files as the prefix followed by a string of unique numbers that increase from one file to the next in the order they were recorded For example 31910001 would be a file recorded at site 3191 The next file recorded will be named 3191002 For the Song Meter ARUs the file names will appear as the prefix followed by a string of numbers which reflect the date and time of the recording i e PARKXXXX_YYYYMMDD_ HHMMSS For example ACAD3191_ 20100528 001856 would be a file commenced at ACAD site 3191 on 28 May 2010 at 12 18 56 AM If the unit was not set up to add a unique prefix to the file name as explained in the installation procedures above then the proper file names must be assigned now to reflect the park site and order of recording or date time as described here
259. on Enter 1 11 11 etc for lower cutoff h hh hhh etc for higher cutoff 1 hhhhh dee Ld 1 139 SOP 7 Acoustic Template Creation Ip LI It This is a trial and error approach and a final value will be subjective When satisfied with the final appearance press Enter 50 100 150 200 250 Shift 0 120 No overlapped cells 317 i 100 No empty cells 33320 J ATTA he Lao Amplitude cutoff lt l 31 1 H a 5 4 r i 60 i pr Tanh Sie i FEE Pe Eg lie a ea 20 Frequency kHz 0 5 1 1 5 2 2 5 3 Time s Figure S7 10 Call 1 after raising the amplitude cutoff from 47dB to 31dB The light gray spectrogram is several time bins to the right of the dark gray spectrogram The next step is to time align the two sound clips Again the R gui prints instructions on how to do this Time shift selection Enter 1 11 11 etc for left shift r rr rrr etc for right shift A 1 dee Aa 1 1 S Enter the commands into the R gui and press Enter 140 SOP 7 Acoustic Template Creation 50 100 150 200 250 300 12 Shift ios 3 120 No overlapped cells a 580 ais 7 100 D 8 No empty cells S Amplitude cutoff t fai dii a i i g ia W 60 F 4 ts le fi Pa 3 Ta me r ATE hee a a F 40 j ETLI TIL a 2 20 0 5 1 1 5 2 2 5 3 3 5 Time s Figure S7 11 Call1 After shifting the light gray spectrogram to the left the number of overlapping cells has in
260. on using each potential template clip as a template In the following example 23 unique song sparrow example songs are saved to a SOSPtemplates directory Each is read into R and a template is constructed and all templates are combined into an object called templates templates lt makeTemplates wave L list sl E users jkatz3 Desktop SOSPtemplates sl wav s2 E users jkatz3 Desktop SOSPtemplates s2 wav s3 E users jkatz3 Desktop SOSPtemplates s3 wav s4 E users jkatz3 Desktop SOSPtemplates s4 wav s5 E users jkatz3 Desktop SOSPtemplates s5 wav s6 E users jkatz3 Desktop SOSPtemplates s6 wav s7 E users jkatz3 Desktop SOSPtemplates s7 wav s8 E users jkatz3 Desktop SOSPtemplates s8 wav s9 E users jkatz3 Desktop SOSPtemplates s9 wav s10 E users jkatz3 Desktop SOSPtemplates s10 wav sl1l E users jkatz3 Desktop SOSPtemplates sll wav s12 E users jkatz3 Desktop SOSPtemplates s12 wav s13 E users jkatz3 Desktop SOSPtemplates s13 wav s14 E users jkatz3 Desktop SOSPtemplates s14 wav s15 E users jkatz3 Desktop SOSPtemplates s15 wav s16 E users jkatz3 Desktop SOSPtemplates sl6 wav s17 E users jkatz3 Desktop SOSPtemplates s17 wav s18 E users jkatz3 Desktop SOSPtemplates s18 wav s19 E users jkatz3 Desktop SOSPtemplates s19 wav s20 E users jkatz3 Desktop SOSPtemplates s20 wav s21 E users jkatz3 Desktop SOSPtempl
261. on about your site including descriptions of any feature described as other such as habitat type tree cover domesticated animals or features that attract animals Additional questions for plant sites Tree cover f there are trees at this site they can best be described as Mostly evergreen trees eg pine or live oak A mixture of evergreen and deciduous trees Mostly deciduous trees eg maple or larch Other describe in comments Slope Is the site on or near a slope No the surrounding terrain is relatively flat Yes in the middle of the slope Yes on the top of the slope or on a ridge Yes bottom of the slope or valley Aspect The slope at this site faces N NE E SE S SW W N Additional questions for animal sites Domesticated animals Which if any domesticated animals are seen outside at the site Cats Dogs Other specify in comments Garden Is there a flower or vegetable garden maintained at the site Yes No Unknown Food water or nest box Are feeders nest boxes or any other features designed to attract animals at the site Bird feeder Fountain or artificial pond Nest box Other describe in comments Fruit 71 Appendix S2 A Datasheets continued NETN Phenology Plant Registrat
262. onse to Adam procedure in Appendix A to rename copies not review Kozlowski originals 227 SOP 11 Data Management and Quality Assurance Quality Control Appendix 11 A Flowchart of Data Management Responsibility Park Coordinator Phenology Observer NETN Data Manager Observations Select and setup sites Collect record observations Enter results into Nature s Notebook Obtain dataset annually from USA NPN Validate dataset for analysis and reporting Image Files Program deploy cameras and reference panels Retrieve data Rename plantcam files Copy files to external hard drives X1 Copy files to PhenoCam server Process image files Audio Files Program deploy ARUs Retrieve data Rename Olympus files adjust for start time Park Coordinator Subsample Olympus files Copy files to external hard drives X2 Process audio files Obtain processed dataset annually for analysis and reporting 229 SOP 11 Data Management and Quality Assurance Quality Control Appendix S11 B Using Bulk Rename Utility software This software can be downloaded at http www bulkrenameutility co uk Main_Intro php P lt Bulk Rename Utility gt loj x Fle Actions Options Help A V 5 Desktop E E My Documents E My Computer E My Network Places g Recycle Bin Archiving Budget BulkRename_Test Dennis Meta Tools H O DeskA
263. ontingency Resources Team Selection Team Fitness Environment Event Evolution Complexity awnowdnaon Ww Ww Total Risk Score 33 Step 4 Identify Risk Control Options Supervision The NETN Phenology Protocol clearly identifies personnel roles and responsibilities and a chain of command At each park the park Natural Resource Manager coordinates the monitoring effort This person is the supervisor and is available to provide training and answer questions from monitoring staff The staff are encouraged to work with a partner in the field but may opt to work alone Monitoring staff visiting remote or hard to access locations are required to follow check in and check out procedures with the park Natural Resource Manager A score of 4 was assigned because of the loose supervision and the likelihood that many monitoring staff will work alone Planning The NETN Phenology Monitoring Protocol includes numerous SOPs that explain training personal safety emergency communication equipment and contacts and appropriate field activities Monitoring staff are asked to review the volunteer manual which summarizes relevant field procedures and provides a summary of the safety SOP and they must sign an acknowledgement that they have reviewed the JSA Monitoring staff are highly recommended to have first aid and CPR training Due to this advance planning written documentation and training procedures a low score 3 was assigned Communication
264. or evaluating photo data Geri Tierney with an observer for cameras aimed at Andrew individual plants Added procedure for Richardson selection of darkness threshold Editorial Michael changes Toomey Steve Klosterman 1 03 May 2013 Geri Tierney Noted future plans to scale up to connect this Michael dataset to satellite imagery Updated Figure 1 Toomey to show Rcc Editorial changes 221 SOP 11 Data Management and Quality Assurance Quality Control Northeast Temperate Network Version 1 12 Overview This SOP describes data management and quality assurance quality control QA QC procedures used to insure accurate data collection by phenology observers and automatic recording devices Data management for three types of data is addressed in this SOP tabular observations digital audio files and digital image files Observation data are submitted to the USA NPN National Phenology Database via Nature s Notebook Audio recordings and image files collected from automatic recorders are stored by staff at participating parks on external hard drives Raw image files also are stored on the PhenoCam server Processed data files from automatic recorders are stored by the NETN data manager until those files can be submitted to the National Phenology Database via Nature s Notebook Responsibility for data management is shared between park coordinators and the NETN Data Manager as shown in Appendix S11 A Data submission Park visitors an
265. oring methods have been incorporated into this protocol Justification Phenology has been recognized as an early indicator of changing climate Root et al 2003 Phenological events respond to variation in cues such as day length temperature and precipitation As the global climate continues to warm and change widespread changes in phenological patterns across the globe continue to occur Parmesan amp Yohe 2003 Parmesan 2006 and altered phenology may have far reaching consequences As species respond individually to changing climate food webs may become uncoupled and competitive relationships altered Miller Rushing et al 2010 For example migrating birds may respond differently to changing conditions than do their key food sources and may arrive too early or too late to find enough food Miller Rushing et al 2008b Invasive exotic species may respond favorably to changing climate conditions and outcompete native species Willis et al 2010 Phenology is particularly well suited to monitoring by citizen volunteers because it is both easy to observe and engaging to the public Phenology is perhaps the simplest process in which to track changes in the ecology of species in response to climate change IPCC 2007 Existing Programs Several phenology monitoring programs already exist in the Northeast and nationwide The Appalachian Mountain Club s AMC Mountain Watch program has been encouraging volunteer monitors to collect phe
266. oring plan might specify that a volunteer will visit a specific designated site e g ACAD site 3191 every other day from April to June and then weekly in July and August and that visits will usually occur in the early morning On each monitoring day monitoring staff must know where they will be monitoring and how they will get there before going into the field At off trail or remote sites the RM DI must be contacted the day before field work will occur and provided with the monitoring staff name cell phone number vehicle license plate number expected parking location s name of the monitoring route and estimated time of arrival and departure from the park Monitoring staff must also establish a check in time for completion of field work If monitoring staff do not check in on or before the planned check in time for completion of field work the RM DI will immediately try to reach them by all available methods If the monitoring staff have not been reached within 30 minutes the RM DI will notify emergency services and initiate a search At ACAD when the NETN PLB and SPOT GPS Messenger are being borrowed by the monitoring staff the trip information must also be provided to the NETN staff members responsible for tracking messages from the devices NETN must also be provided with the RM DI name phone number and e mail and the RM DI must be provided with contact information for NETN staff If the survey is cancelled or if the plan changes
267. ork contact the Natural Resource Manager for assistance For contractors and cooperators follow your organization s procedures for documenting accidents and notify the NETN program manager with details of the incident 37 SOP 1 Safety Non Emergency Incidents 1 Contact the park Natural Resource Manager immediately after incident The park Natural Resource Manager will inform NETN staff 2 For NPS staff and volunteers complete Worker s Compensation paperwork must be done within 48 hours of incident contact the park Natural Resource Manager for assistance For contractors and cooperators follow your organization s procedures for documenting accidents and notify the NETN program manager with details of the incident 3 Seek medical attention if needed NOTE Never discard original paperwork related to workers compensation claims including information from doctor s visits CA 1 CA 2 CA 16 or CA 17 forms Field Preparation Everyone participating in phenology monitoring is responsible for maintaining a safe work environment for themselves and others Job Safety An important tool used to promote safe conduct is the Job Safety Analysis JSA sometimes called a Job Hazard Analysis or JHA This approach is consistent with NPS Directors Order 50 and Reference Manual 50B for Occupational Health and Safety The JSA process is to 1 identify hazards associated with field and laboratory settings as appropriate and 2 dev
268. ot use spaces slashes colons semi colons periods or commas as they may cause operating system or R errors when written to files Eleven non exhaustive example calls to create templates are provided below followed by a sequence of resulting spectrograms Screen captures of some steps are omitted to save space During these calls the R gui will offer prompts such as the one below with the actions initiating the prompt change in italics Rectangular selection Select upper left corner of rectangle with a left click Right click to exit first left click Select lower right corner of rectangle with a left click second left click Select upper left corner of rectangle with a left click Right click to exit right click Done 126 SOP 7 Acoustic Template Creation Call 1 change only the selection type from the default point BTNW_rect_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav select rect Call 2 use a descriptive name BTNW_rect_MandHnotes_C lt makeCorTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav select rect 20 40 6 80 100 120 Sn a a a _ 9 l l 9 seo mi 180 8 los 160 o 160 77 q I a T 140 140 6 gt 6 z 120 amp 120 v 5 5 _j 5 7 i 3 Bs 100 2 100 u hi 4 4 om 80 80 37 60 a 60 2 T T T 2 T T T i 0 5 1 1 5 2 25 0 5 1 1 5 2 2 5 Time
269. otocol and is included as an appendix Appendix A Additionally a Job Safety Analysis JSA which documents hazards associated with this protocol and recommends approaches to mitigate these hazards is included as an appendix Appendix B to this SOP The JSA must be read and signed by all monitoring staff who conduct field work for this protocol Forms that go along with this SOP Safety Acknowledgment Safety Checklist and Trip Plan are provided in Appendix C This SOP does not cover first aid This SOP is written to provide general guidance that should be applicable for most parks The park Natural Resource Manager is responsible for ensuring that all volunteers or other monitoring staff have up to date emergency contact numbers directions to medical facilities and other park specific safety information Responding to an Incident Life Threatening Medical Emergency 1 Call 9 1 1 or park emergency number Administer first aid to the best of your knowledge ability and training If appropriate transport to emergency room Directions to the nearest hospital from each park and park specific emergency contacts procedures will be provided to each volunteer by the park Natural Resource Manager 2 As soon as it is practical to do so inform the park s emergency contact provided by the park Natural Resource Manager The park Natural Resource Manager will inform NETN staff 3 For NPS staff and volunteers complete Worker s Compensation paperw
270. ource Manager with seasonal schedule of monitoring Discuss safety issues and bring up any concerns with park Natural Resource Manager Safety and emergency procedures Emergency contact s Assistance finding monitoring partner for remote or hard to access sites Verify that you have needed gear Clipboard data sheets timer pens pencils Cell phone or other communication device e g SPOT GPS Messenger at Acadia Suitable field clothes and personal gear e g insect repellent food water rain gear First aid kit highly recommended Camera and audio recorder gear and supplies if conducting photo or acoustic monitoring One to two days before field work Complete trip plan for remote or hard to access sites and send it to the park Natural Resource Manager or designated individual If using SPOT GPS Messenger or Personal Locator Beacon at ACAD check out the equipment and review procedures and send trip plan to NETN staff responsible for tracking traffic from these devices Verify that the trip plan has been received Check weather forecast and adjust plans accordingly Day of field work Notify park Natural Resource Manager or designated individual RM DI of any changes to your plans to visit remote or hard to access sites Notify a trusted person spouse friend co worker etc of your planned visit to designated accessible park site Check in on arrival to remote or hard to access site if requested by park Natural Resource Manager or design
271. ouser com 161 3507 E 3507 E qs itG3xFeL 1F1sDGBg7GCnYak r 2 1 00 52bj3wF 252b70i 252buskoQVEw 3d 1120NF Guard Box Protector B amp H Photo http www bhphotovideo com c product 150620 1 Watertight Case www bhphoto PE1120B REG Pelican 1120 001 110 1120 Case without F 17 95 without Foam video com oam html Black 32GB microSDHC B amp H Photo http www bhphotovideo com c product 738454 1 Memory Card www bhphoto TRMSDC232GB REG Transcend TS32GUSDHC2 32GB microSDHC 72 63 y Car A video com Card html 5 32GB SDHC B amp H Photo http www bhphotovideo com c product 592772 1 www bhphoto KISDHC432GB REG Kingston SD4 32GB 32GB SDHC Memory C 66 95 Memory card A video com ard html i Ameri Rack 45 eae to SD Technology In PA TEC1 T ee ae 24 35 MAHA PowerEx 4 1 2V11000mAhD Zbattery com MH 2D110 eS ee 50 70 Cell NiMH Batteries 11000mAh D Cell NiMH Batteries 2 Card 1 Costs are for the quantity needed for one recording unit in 2011 In many cases costs per recording unit can be reduced by buying in bulk Two choices of recorder are listed the DM 420 is the one used in units built by NETN to date The DM 620 allows for recording in WAV which requires more memory for a given recording length but produces higher quality files 3 Two choices of microphones are listed the microphones from Mouser com are the ones used in units built by NETN to date The NPS Night Skies and Natural Sounds Program highly recommends
272. p and you have created appropriate file names for all photos you will be able to transfer images via anonymous FTP to our site For users comfortable with using the command line interface we suggest doing so in a terminal window in UNIX based machines such as UNIX LINUX Macs or Cygwin in Windows machines Directions are below For those who are not directions for using a free FTP client are below Using a terminal window The URL for the ftp directory for your site will be ftp phenocam sr unh edu data sitename 233 SOP 11 Data Management and Quality Assurance Quality Control Appendix S11 C Instructions for transferring images to the PhenoCam Server via FTP continued For the purposes of illustrating a transfer we will just use a test folder called ftptest or ftp phenocam sr unh edu data ftptest To connect to PhenoCam ftp site via Windows Explorer on a Windows 7 computer 1 Open Windows Explorer right click the start button and select Open Windows Explorer A Libraries gt 4 Search Libraries Fie Edit View Tools Help Organize Newlli Fe Favorites E Desktop IP My Documents lB Downloads Google Drive T Recent Places Ga Libraries E Documents a Music E Pictures B Videos jE Computer amp Local Disk C gt Local Disk D mitchellbr inp NETN Test Web f S NETN Staging W amp NETNZ Drive Ji ftptest on
273. pheno 4 items ibrary Libraries Open a library to see your files and arrange them by folder date and other properties Documents Music lt p library LD ley Videos Library Pictures Sp library 2 Select Tools Map Network Drive Specify the di Drive Folder rive letter for the connection and the folder that you want to connect to P i Example server share V Reconnect at logon Connect using different credentials Connect to a Web site that you can use to store your documents and pictures Finish f em What network folder would you like to map 3 Click on Connect to a Web site that you can use to store your documents and pictures 234 SOP 11 Data Management and Quality Assurance Quality Control Appendix S11 C Instructions for transferring images to the PhenoCam Server via FTP continued Welcome to the Add Network Location Wizard This wizard helps you sign up for a service that offers online storage space You can use this space to store organize and share your documents and pictures using only a web browser and Internet onnection You can also use this wizard to create a shortcut to a website an FTP site or other network location 4 Click Next Where do you want to create this network location Choose a custom network locaton liag Spetity the address of a website
274. plate is developed The R platform and package we have developed definitely has a learning curve but so does the process of building recognizers in Song Scope This SOP describes wildlife recording file management the use of R for extracting sound events from the recordings turning digital sound files into ecological data and archiving sound events Sound events from birds frogs and other taxa are detected and classified using spectrogram cross correlation and or binary point matching The resulting dataset is a times series of phenophase detections SOP 7 Acoustic Template Creation describes the process of developing templates used in this SOP Overview of full data collection and analysis process 1 Determine the survey schedule and number of sites to monitor see SOP 2 Site Selection and Set Up and SOP 6 Deployment and Maintenance of Autonomous Recording Units 2 Purchase or build suitable recorders batteries and recording media see SOP 5 Building an Autonomous Recording Unit and SOP 6 3 Set up a computer workstation to perform the sound processing purchase sufficient local disk storage or network disk storage see SOP 11 Data Management and QA QC 157 SOP 8 Automated Sound Detection and Classification 4 Construct a MySQL database and local file system to store recordings and or results herein and Appendix S8 A and S8 B discuss with NETN data manager 5 Determine maintenance interval based on survey sched
275. plates n peaks n hits min score max score BINWd1 0 209 19 0 00578 0 789 BTNWpartial 192 22 0 03410 0 806 BINWd 8 218 18 0 01300 0 783 BINWd 5 218 19 0 01370 0 786 BINWd 2 213 20 0 04950 0 785 BTNWauto 8 187 LS 0 03310 0 647 BTNWauto 2 193 14 0 04490 0 648 Verifying Results A subset of the data is manually verified for proper identifications This may be performed under the direction of NETN staff rather than by park coordinators Verifying the results serves three purposes 1 Evaluate the automatic score cutoff used when scanning surveys 2 Observe of patterns of misidentification of templates 3 Construct hit densities for likelihood analysis The three ways of verifying the detections and classifications are looking at spectrograms while listening to individual hits within the hits list using the showPeaks function viewing annotated spectrograms of the survey using the SCTPlot function and viewing spectrograms of all hits side by side using the collapseClips function Verifying individual hits via spectrograms and playback The arguments for the showPeaks function include scc pks L and which one these feed the data in from sccCor and findPeaks and identify the template to be verified The argument t lim allows just a portion of the hits to be verified by specifying the start and end times in seconds The flim argument customizes the spectrogram y axis The verify argument controls the interactive verification proc
276. polarities SOP 5 Building an Autonomous Recording Unit recording units as they are oriented in the picture to the right with polarities properly aligned Insert four D batteries into the battery holders and check that the recording unit powers on Prepare the internal audio connector Cut a 13 section of shielded audio cable Strip back 1 of the outer insulation and remove the mylar to expose the shield lead image at right Strip back 3 8 of each audio conductor Orient the Pelican case with the hinge on the right and the lid in front Drill a 5 32 hole in the bottom center of the Pelican case and pass 2 of audio cable through Solder one conductor to the R terminal and the other conductor to the L terminal of the female phono jack Solder the shield to the terminal Drill three 1 8 holes in the Pelican case in a triangle beneath where the phono jack will sit one under the threaded barrel and one to either side see pattern below Pass a 4 cable tie through the side holes and loop another through the hole beneath the barrel see drawing below right Use the cable ties to pull the phono jack tight against the Pelican case On the other end of the audio cable slide the male phono plug housing onto the cable Strip back 1 2 of the outer insulation remove the mylar the shield isolate the shield lead and strip back 3 8 of each audio conductor Again solder one conductor to the R terminal and th
277. posure to the sun by wearing sunscreen and or protective clothing Monitoring staff should always carry ample water 2 3 liters for travel to remote or hard to access sites and food when working in the field Dehydration is a serious condition that can lead to more serious conditions if untreated and should be avoided It is important to drink liquid frequently to maintain hydration on a warm day even if you don t feel thirsty Field Safety Slip Trip Fall Prevention Uneven terrain slippery rocks dense brush and fatigue are all hazards that could result in a slip trip or fall The following guidelines should be obeyed by monitoring staff to avoid injury from slips trips or falls e Always wear appropriate footwear such as sturdy hiking boots e Pay attention to where you are going and remain alert of potential hazards e Walk at an appropriate pace and adjust pace for changes in terrain e g slow down and take smaller steps on slippery surfaces e When hiking long distances take breaks to avoid fatigue e When navigating to a location off trail choose the safest route this may not be the shortest route Avoid river crossings excessively steep terrain and sudden drop offs Always be careful when navigating over piles of scree and alert others of falling rocks Proper use of Backpacks Monitoring staff may carry a day pack with personal gear water and clipboard weighing more than 20 pounds and it is important for eve
278. r D cell batteries ____ Take out the full SD cards and replace with empty SD cards ____ Record SD card numbers in datasheet ____ Reset the recorder for a new 24 hour or other desired recording schedule ___ Record start time for recording schedule ____ Check the packet of desiccant and___ replace if necessary ____ Check the unit and cables over for any damage or needed adjustments ____ Remember to shut all units and battery cases 111 SOP 6 Deployment and Maintenance of Autonomous Recording Units Appendix S6 B Unit Specifications Olympus Unit Specifications Exterior High impact structural copolymer polypropylene Exterior Dimensions 8 12 x 6 56 x 3 56 20 6 x 16 7 x 9 0cm LxWxH Microphone Cable Length Variable Microphone Cable Shielded Yes Microphone Impedence 2 2 K Ohms Microphone Directional Properties Omnidirectional Microphone Operating Voltage 2 V Microphone Sensitivity 40 dB 3 dB Recording Formats Linear PCM MP3 WMA Recording Input Level Mic Sense Middle 60 dBv Recording Input Impedence 2 2 kQ Recording Power Input D cell battery 2 4 V 9 11 amps Recorder Operating Temperature 0 C 42 C 32 F 107 7 F Recorder Overall Frequency Response See table below Recorder Plug In Power 0 8 V 2 5V Maximum Recording Times Based on Storage Media MP3 Format Recording Mode 8GB micro SD 16GB microSD 32GB micro SD Card Card Card 320 kbps 54h 108 h 216 h 256 kbps 68h 132 h 264 h
279. r available time getting to proper medical treatment facilities than it is to fumble with field therapy and wait for assistance to reach you The range of the copperhead covers the following NETN parks Appalachian NST APPA Morristown NHP MORR Roosevelt Vanderbilt NHS ROVA Saratoga NHP SARA and Weir Farm NHS WEFA The likelihood of encountering a copperhead is low in NETN parks although higher along the southern portions of APPA Copperhead bites are not typically considered life threatening and in most cases antivenin is not administered The range of the cottonmouth covers the southern portions of APPA Cottonmouth bites that are defensive typically do not contain venom However cottonmouth snakes are capable of delivering a lethal dose The range of the timber rattlesnake covers all NETN parks except ACAD This species is listed by NatureServe as critically imperiled S1 New Hampshire Vermont Massachusetts and Connecticut or vulnerable S3 New York Pennsylvania throughout NETN and the likelihood of encountering a timber rattlesnake in NETN parks is very low although higher along the southern portions of APPA Adult timber rattlesnakes are capable of delivering a lethal dose of venom Bees Wasps and Yellow Jackets If any monitoring staff are allergic to bee stings they should alert their colleagues and make sure to carry appropriate medications If they carry an epinephrine injector and are working in a team th
280. r species using a quick loop One of the easiest loops to write is the for loop which will allow each file name to include the species and the survey The syntax of the loop is for i in vector do function for i in l length event rec writeWave event rec i file paste E users jkatz3 Desktop SARA3_A_062610_ names event rec i wav sep To store an output key add the argument return times to the bindEvents call event rec lt bindEvents rec E users jkatz3 Desktop BTNWtemplates SARA3_A_062610 wav file SongScope ExampleEventList csv by species TRUE parallel FALSE return times TRUE Adding this argument adds a new element to the output list called times and moves the wave files to a lower level in the list gt names event rec 1 times wave gt names event recStimes 1 AMCR AMGO AMRO BAWW BTNW CEDW COYE GCFL GRCA OVEN 1 t REVI RWBL SCTA SOSP WAVI WIWR YWAR gt names event recSwav 1 AMCR AMGO AMRO BAWW BINW CEDW COYE GCFL GRCA OVEN 1 1 REVI RWBL SCTA SOSP WAVI WIWR YWAR You can write the wave object to a file using an almost identical loop but specifying the item in the list for i in 1 length event recS wave writeWave event recSwave il file paste E users jkatz3 Desktop SARA3_A_062610_ names event recSwave il
281. r wetland Spruce fir forest Alpine and Subalpine Spruce fir forest Alpine and Subalpine Northern hardwood forest Spruce fir forest Alpine and Subalpine Grassland Grassland Coastline Coastline Coastline Table 2 Animal species selected for phenology monitoring in NETN designated park habitats Animal species Lifeform Designated habitat Spotted salamander MIP Ambystoma maculatum Amphibian Vernal pools Spring peeper re Pseudacris crucifer Ampnpian Vernal pools Wood frog sat Vernal pools Rana sylvatica AMmpnIpian Permanent freshwater wetland Common loon Bird Permanent freshwater wetland Gavia immer Coastline Great black backed gull Bird Coastline Larus marinus Bobolink Dolichonyx oryzivorus Bird Gr ssland Bobolink Dolichonyx oryzivorus alle Grassland Red winged blackbird Bird Grassland Agelaius phoeniceus Monarch butterfly Insect Lepidoptera Grassland Danaus plexippus Eastern tent caterpillar Malacosoma americanum Ovenbird Seiurus aurocapillus Winter wren Troglodytes hiemalis Insect Lepidoptera Bird Bird Northern hardwood forest Northern hardwood forest Spruce fir Forest To accomplish these objectives NETN uses three approaches 1 park visitors are recruited on site to submit one time phenological observations at marked locations 2 interested volunteers and park staff are recruited and trained to submit repeat phenological observa
282. rity with relevant SOPs from this protocol The majority of monitoring observations are collected by volunteers This program offers three levels of volunteer engagement allowing participation by a wide range of potential volunteers First park visitors are recruited on site to submit one time or initial observations Second interested volunteers are trained to submit repeat observations This level requires a moderate at least weekly time commitment some familiarity with plant identification and observation and the ability to keep careful records Third volunteers with technical skills and interest may be trained to assist with maintenance or data collection from automated recording devices Training Procedures Volunteers interested in making repeat observations attend a 1 to 3 hour training session held annually at each participating park and within each APPA region When possible the NETN Science Communication Specialist will host this training during annual park visits Training 19 focuses on understanding material in the NETN Phenology Observer Training Manual and includes a brief introduction to phenology locations of designated monitoring sites description of monitored species and phenophases and directions for submitting data online as described in the Observer Recruitment and Training SOP 20 Operational Requirements Annual Workload and Field Schedule The annual workload for NETN phenology monitoring will depend upo
283. rk images taken at night being one low DN peak and most of the daytime images forming a high DN peak In Figure 1 the threshold can then be set to filter out the low DN images by choosing a data point just above the lower peak of night images and calculating the full sun of this data point Calculate of maximum DN as total brightness of this data point sum of R G and B DN divided by maximum DN 256 256 256 768 then round to the nearest 5 218 SOP 10 Processing Image Data Figure 10 1 illustrates this procedure Note the bimodal distribution the lower peak represents nighttime photos and the higher peak represents daytime photos Using the breaking point 100 we can estimate a day night threshold of 100 768 or 13 round to 15 for the PICP 1400 r r r r r In PCIP set dark thres in the calculation window to be 15 or to the level indicated by analysis of the frequency distribution as described above 1200 1000 o i T In addition PCIP allows the user to select minimum and maximum hours of image to include in analysis Under Calculation Options choose a minimum of 4 i e 4 am and a maximum of 20 i e 8 pm Frequency 3 o 0 50 100 150 200 250 300 350 Total brightness Assigning per90 Figure S10 1 Frequency histogram of total To further reduce the influence of short term image brightness R G B for one year of changes in scene illumination due to weather
284. rname CoopUnit CPU as P amabian Internal DNS hostname i 7 AREN int instance db xeround com 19055 Connections as reation Date 2012 10 1 Size 10 MB Data Center Amazon EC2 US Clicking on the hostname would connect you to your instance with Auto Scale Disabled Learn more East Virginia phpMyAdmin To create the database described above click on the link called Create New in the top right hand menu and then select the database size you d like We selected the free 10MB version to test this protocol You may need more space if this becomes your actual working database Note that Xeround offers only one free database instance per user 183 SOP 8 Automated Sound Detection and Classification Appendix S8 A Creating a MySQL database continued New DB Instance x Step 1 of 3 Xeround FREE Xeround BASIC Xeround PRO Up to 10MB Up to 0 5GB Up to 20GB SELECT gt SELECT gt SELECT gt Shared Environment Shared Environment Dedicated Environment High Availability Guaranteed High Availability Guaranteed multitenant Throughput up to 1MB s Throughput up to 8MB s High Availability Guaranteed Connections up to 5 Connections up to 40 Auto Scaling SSL Support Throughput Unlimited Spain Connections up to 4 800 See plans and prices ae Hot Backups See plans and prices for larger database Contact us Once you have selected a plan you will select a Data Center the location in the cloud th
285. rney Added filenaming guidance and specific settings for TimelapseCam 1 02 Nov 2012 Andrew Replaced Appendix B with reference to Richardson PhenoCam document Included file naming Michael procedure Editorial comments Toomey Geri Tierney Steve Klosterman 1 10 May 2013 Geri Tierney Reduced frequency of images from plant cams Response to Michael and other cameras aimed at individual plants review Toomey Clarified need for frequent images for canopy Reference Andrew photos Added table relating camera FOV panel Richardson image size distance to target and resolution procedure revised as per A Richardson s ongoing research 212 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras Appendix S9 A Camera Deployment Metadata Equipment Camera s Writing utensil Empty SD cards Charged batteries Camera housing for webcams Laptop for webcams Mounting bracket optional for Wingscapes plant cams Mounting pole tripod or straps for Wingscapes plant cams Colorchecker card Reference panel with mounting hardware Tools for mounting Date Location Park Site Lat Long Camera make model Camera serial or unit number View target canopy or plant Plant species in view Monitored plant ID if any What direction is the camera pointing north is preferred For webcam what is the internet connection and camera address What power source or specific battery type d
286. round com The steps are likely to be very similar if you use other formats You can create an account at Xeround and then log in with your email and password eround The Cloud Database Xeround SQL Cloud Database Login to Your Account Don t have an account Email Be up amp running with your MySQL database in the Cloud in minutes Password Xeround s cloud database is an elastic always on database that lets you run your existing MySQL based application in the cloud Auto Scaling SUBMIT gt Ensure High Availability Available for both public and private clouds No code changes required to your app Forgot Password Login Problems Create Your Cloud Database Today Ask Us SQL Cloud DBaaS About Us ContactUs Terms and Conditions Privacy Policy 2012 Xeround Inc Once you ve logged in you will see a list of your databases in the DB Instance Manager We have created a database called Acoustics Information about the database is shown in the lower panel DB Instance Manager gt Create New Drop amp Backup 4 Export Change Plan Name Plan Status Data Size Mb Ops s Cpu Connections Acoustics Xeround FREE w Healthy O 0 0 0 O 0 Acoustics Acoustic Monitoring 2 Ca x Instance ID 29243 v3 2 1 112 Connecting to your DB Instance Thresholds v E 80 pa Plan nem ree External DNS hostname Data Size i haat instance db xeround com 19055 60 95 Use
287. row 2 has a color of Ra Ga Ba while for camera B the same square has a color of Rg Gp Bg Then color data for a vegetated region of interest from camera A can be re scaled to match the color balance of camera B by multiplying the red channel by Rp Ra the green channel by Gp Ga and the blue channel by Bg B a Note that this re scaling is not strictly necessary for successful analysis and re scaling can be applied at a later time as long as the metadata described above are available To check changes in the camera s color sensitivity over time e g consider A and B not as different cameras but as measurements at the start and end of the growing season In this case the analysis focuses on changes in the relative sensitivity of R G and B color channels e g R to G G to B or R to B If any of the ratios Ra Ga Rp Gp Ga Ba Gp Ba or Ra Ba Rp Bg are lt 0 9 or gt 1 1 then the camera is a candidate for replacement as shifts over time in the sensitivity of different color channels will make data interpretation challenging The second objective of monitoring day to day variability is met by mounting a small reference panel in the camera s field of view so that the panel is included in every picture Figure S9 3 Unfortunately changes in illumination geometry and the effects of this on panel brightness and apparent color make it difficult to use the reference panel as a true standard i e that can be used for post
288. rrent cutoff 31 T Enter Select on points with left mouse click To continue right click 25 left clicks right click 25 selected Select off points with left mouse click When done right click 73 left clicks right click 73 selected Done 135 SOP 7 Acoustic Template Creation Call 1 using rect selection and the default density and buffer values BTNW_rect_d100_B lt makeBinTemplate clip C Users jkatz3 Dropbox LabDemo Templates BINW wav t lim c 0 2 8 frq lim c 2 9 select rect binary TRUE 20 40 60 80 100 120 9 li l ji l i Amplitude cutoff 31 E 180 piituqe Cuto 180 8 amp OT N 140 140 x J 6 rey ros 120 A m 120 rT 5 s 54 z 100 A tO Ww ral 80 f 80 60 34 m 60 2 T T T T 0 5 1 1 5 2 2 5 Time s 20 40 60 80 100 120 se DO O O A 9 9 l l l l l l L 180 a 180 A 160 l 160 7 gt 74 L140 L 140 gd 6 4 a 120 M 120 D 5 54 gt 57 gt E g 100 2 100 j E 44 4 7 ie 80 f 80 a a 60 2 i i i i i 2 T T T T 0 5 1 1 5 2 2 5 0 5 1 1 5 2 2 5 Time s Time s Figure S7 5 Top left with binary TRUE the template opens with a default amplitude cutoff of 51dB plenty of noise is visible over the cutoff Top right after raising the cutoff to 31dB only signal remains visible Bottom left call 1 dens 1 and buffer 0 after on po
289. rs wm Queue empty The file transfer should go relatively quickly and there will be status messages for each photo in the status window Again because the file listings are locked you will not see the individual files displayed on the Remote server side 240 SOP 11 Data Management and Quality Assurance Quality Control Appendix S11 C Instructions for transferring images to the PhenoCam Server via FTP continued phenocamFTP phenocin sr unh edu FileZilla a ACE ss a axe va Username Password z TUAJ E OIIE GUE TIE T ENI AI IEN S rvard_2012_08_01_093138 jp9 150 Ok to send data n 226 Transfer complete File transfer successful transferred 326 5 KB in 1 second 226 Transfer complete File transfer successful transferred 320 9 KB in 1 second Retrieving directory listing Command PASV 227 Entering Passive Mode 132 177 243 160 77 131 LIST 550 Permission denied Failed to retrieve directory listing media pheno archive harvard 2012 08 Remote site data ftptest 07 8 408 data i ftptest Filename harvard _2012_08_01_040137 jp9 Filename Filesize Filetype Last modified Permission Owner Gro harvard_2012_08_01_050137 jpg harvard_2012_08_01_053137 jpg harvard_2012_08 01_060137 jp9 harvard_2012_08_01_063137 jpg harvard_2012_08_01_070137 jpg harvard_2012_08_01_073137 jpg harvard_2012_08 01_080137 jpg Directory listing Failed Selected 12 files Total size 3 5 MB Empty director
290. rs Boston MA Crimmins M A and T M Crimmins 2008 Monitoring plant phenology using digital repeat photography Environmental Management 41 949 958 Denny E G K L Gerst A J Miller Rushing G L Tierney T M Crimmins C A F Enquist P Guertin A H Rosemartin M D Schwartz K A Thomas and J F Weltzin Submitted Standardized phenology monitoring methods to track plant and animal activity for science and resource management applications Journal of International Biometeorology Gazal R M A White R Gillies E L I Rodemaker E Sparrow and L Gordon 2008 GLOBE students teachers and scientists demonstrate variable differences between urban and rural leaf phenology Global Change Biology 14 1568 1580 Goulart M F J P L Filho and M B Lovato 2005 Phenological variation within and among populations of Plathymenia reticulata in Brazilian cerrado the Atlantic forest and transitional sites Annals of Botany 96 445 455 Howard E and A Davis 2009 The fall migration flyways of monarch butterflies in eastern North America revealed by citizen scientists Journal of Insect Conservation 13 279 286 IPCC 2007 Climate Change 2007 Impacts Adaptation and Vulnerability Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change Cambridge University Press Cambridge Kasten E P S H Gage J Fox W Joo 2012 The remote environmental assess
291. rtain amount of technical support but they also have a higher price tag about 800 for the unit batteries and memory cards Do it yourself ARUs are significantly cheaper and offer a potential learning experience e g for a high school science class for about a quarter the price This SOP provides specific procedures for constructing an inexpensive autonomous recording unit ARU using an Olympus digital audio recorder housed within a weatherproof Pelican case and connected to an array of two microphones Power is supplied by a battery pack of 4 D cell batteries and data is stored on an SD card The ARU is a compact weather resistant autonomous field recorder with three independent timer settings It is designed to be temporarily attached to a tree or post using long cable ties cable straps or rope and the microphone is designed to hang 2 3 from the recorder The recorder produces high quality two channel left right MP3 or WAV recordings onto removable SD or microSD media The channels are intended to be identical to provide redundancy in case of physical damage or water intrusion into one channel A recorder s battery will allow deployment for as long as 28 days of 24 hour per day recording As of 2012 media constraints allow for a maximum equivalent of 13 days of 24 hour per day recording onto a 32GB SD or microSD card This procedure was developed by and Jon Katz and Corinne Brauer of the Vermont Cooperative Fish and Wildlife Res
292. rticipate at optimum frequency Sites with automated cameras or audio recorders collect data frequently or continuously throughout the day providing a data stream at optimum frequency For plant observations at least three individuals of each plant species are marked and monitored at each site Monitoring the same individuals repeatedly over time limits the influence of confounding factors such as genotype and microclimate that might affect observations of different individuals over time However it is impractical for volunteers to mark and monitor individual animals so animal species are monitored as a population at each site Monitors observe and record phenological status and abundance using Nature s Notebook Phenophase definition sheets and datasheets Observers may be untrained park visitors recruited by information displays during a park visit to make one time or initial observations or park volunteers trained to make repeat observations throughout the season Observers upload data directly into Nature s Notebook www nn usanpn org Automated recording units are deployed in some parks to detect vocalizations of bird amphibian and other species of interest Raw audio files are processed using spectrogram cross correlation or binary point matching to detect and classify phenophase status The resulting processed data set is a time series of phenophase detections Digital time lapse photography is used to track seasonal development
293. ructions above for SM1 but rather than connecting the voltage regulator to the battery holder instead make all connections to the appropriate external power in wires Note that the pictures below are of an SM1 118 SOP 7 Acoustic Template Creation Northeast Temperate Network Version 1 01 Introduction There are a variety of tools available for automatic detection of species on audio recordings Among these perhaps the best known is the Wildlife Acoustics Song Scope platform which uses a Hidden Markov Model algorithm with carefully developed recognizers to detect species on field recordings After much consideration we decided not to use Song Scope for the following reasons 1 Song Scope is a black box and it is not clear exactly what the recognition algorithm does 2 Song Scope recognizers can only be built by many rounds of trial and error and tweaking numerous parameters Building recognizers is an art not a science 3 Song Scope is not suitable for long term monitoring since regular software updates alter the recognition algorithm and require complete reanalysis of all prior data to ensure consistency 4 Song Scope is expensive especially for a program intended to run in a distributed fashion with many people running analyses NETN staff and cooperators decided that the best approach would be to use simple algorithms spectral cross correlation and binary point matching While the implementation is per
294. rver instance29243 db xeround com via TCP IP acoustics x Software MySQL E Server connection collation 4 utf8_general_ci gt information_schema Software version 5 1 42 Source distribution mysql Protocol version 10 User CoopUnitq 23 21 60 69 Server charset UTF 8 Unicode utf8 4 amp Language English Theme pmahomme Fontsize 82 Apache 2 4 2 Unix OpenSSL 1 0 0 fips PHP 5 4 3 Database client version libmysal mysqind 5 0 10 20111026 id More settings bOb3b 15693 fGaebIaa66b6461e0e3391175039 PHP extension mysqli amp Version information 3 5 1 Documentation Wk Official Homepage Contribute Get support List of changes This section is called phpMyAdmin and you can think of it as the main page for working with your database In the left menu you can see the name of the database you created acoustics Notice also the menu at the top of the panel Poke around to get a feel for what s what if you get lost just click on the phpMyAdmin logo and you Il be brought back to this home page To add the tables previously described to your database copy the schema from Appendix B Press the SQL tab and paste it in to the text window and press the Go button in the lower right corner This code will create the tables described above add in table and column descriptions and assign keys to each table 187 SOP 8 Automated Sound Detection and C
295. ry y Unique w More T Check All Uncheck All With selected _ Browse Change Drop Ped Primary W Unique E Index If yov d like to insert some records to your database you can click on the Insert tab and try it out However we will hardly be using this interface at all from this point on Yow Ill use Microsoft Access as a front end to enter data into the database and you ll also use R In order to allow these program to work with your new database you ll need to create an ODBC connection on your computer and we ll do that next Setting up an ODBC Connection To let your computer interface with your new MySQL database you ll need to set up an ODBC connection Open Database Connectivity Here s how 1 Windows Operating Systems a In Windows search for ODBC Data Suisse Administrator gt ODBC Data Source Administrator B User DSN System DSN File DSN Drivers Tracing Connection Pooling About User Data Sources Name Driver dBASE files Microsoft Access dBASE Driver dbf ndx Remove ENEE Excel Files Microsoft Excel Driver ads xdsx xdsm x MS Access Database Microsoft Access Driver mdb accdb Rover SQL Server Native Client 10 0 r An ODBC User data source stores information about how to connect to I the indicated data provider A User data source is only visible to you and can only be used on the current machine
296. ryone to understand appropriate ways to pack lift and carry a backpack to avoid back neck and shoulder injuries Monitoring staff should follow these guidelines especially if carrying more than 30 pounds Use a sturdy field pack with padded and adjustable hip and shoulder straps Pack heavy items in the center of the pack and close to your back Make sure weight is evenly distributed from side to side Once equipment is packed tighten the compression straps to minimize movement inside the pack during travel 40 SOP 1 Safety e When picking up a heavy pack use your legs to do the lifting and use slow smooth movements Keep your back straight and keep the pack close to your body Do not twist or bend at the waist and do not swing the pack quickly over one shoulder e Always carry a pack with both shoulder straps and with the hip belt and chest straps secured e The pack should be positioned near the center of the back and most of the weight should rest on your hips e Keep your pack organized and only carry the necessary equipment food and water to reduce weight Weather Weather conditions in the eastern U S can be hazardous and can change quickly Monitoring staff are responsible for planning their day according to the local weather forecast and for being aware of their surroundings and changing conditions Thunderstorms Storms that produce strong winds and lightning are dangerous and should be avoided in the field
297. s information sheets which are available for download from the Nature s Notebook website www nn usanpn org Table A 1 Monitored phenophases for deciduous trees and shrubs USA NPN Phenophase Red maple Sugar maple Hobblebush Beach rose Breaking leaf buds Leaves Increasing leaf size Colored leaves Falling leaves Flowers or flower buds Open flowers Pollen release Fruits Ripe fruits Recent fruit or seed drop X X X X X Table A 2 Monitored phenophases for evergreen conifers USA NPN Phenophase Breaking needle buds Young needles Pollen cones Open pollen cones Pollen release Unripe seed cones Ripe seed cones Recent cone or seed drop Balsam fir X 31 X Table A 3 Monitored phenophases for wildflowers and forbs USA NPN White Garlic Common Rough Painted Bunch Marsh Purple Beach Phenophase wood mustard milkweed stemmed trillium berry marigold loosestrife pea aster goldenrod Initial growth X x x x x x x x x Leaves x x x x x x x x x Flowers or x x x x x x x x x flower buds Open flowers x x x x x x x x x Pollen release Fruits x x x x x x x x x Ripe fruits x x x x x x x x x Recent fruit or x x x x x x x x x seed drop Table A 4 Monitored phenophases for seaweed Rockweed USA NEN Phenophase Ascophyllum nodosum New side branches x Receptacles x Flat receptacles x Smooth inflated receptacles x Dotted inflated receptacles x Torn receptacles
298. s Determination of species specific detection probabilities using automated methods is in progress Save the schedule you create to the highest root directory of an SD card and load it into the recorder during setup as described at the bottom of this page Be sure to either save the schedule to all cards or load the card with the schedule into slot A of the Song Meter 104 Days Between Card and Battery Swaps e N b 224 Days Between Card and Battery Swaps He N SOP 6 Deployment and Maintenance of Autonomous Recording Units WACO Compressed Exclusive Bat Recording SM2 Battery Life Available Deep Cycle Storage Available 128GB 192kHz mono SM2 Battery Life Available D cells Storage Available 32GB 192kHz mono i ES RS S4 S ar e SS eS SS Sees mee ats ees a ae mp me ee oem ae 5 10 15 20 25 30 35 40 45 Minutes recorded per hour WACO Compressed Night Bat Recording Day Bird Recording SM2 Battery Life Available Deep Cycle Storage Available 128GB SM2Battery Life Available D cells Storage Available 32GB m eS SS eS ee ES SE ee Sea ee ae a 5 10 15 20 25 30 35 40 45 50 55 60 Minutes recorded per hour Figure S6 7 Days of SM recording ti
299. s These include selecting plants that appear to be healthy undamaged and free of pests and disease When selecting multiple individuals of a species at a single site we select individuals that are growing in a similar environment but are not direct neighbors in order reduce the likelihood that selected individuals are genetically identical Animals are not monitored as individuals It is impractical for volunteers to mark and monitor individual animals so animal species are monitored as a population at each site as described in the Observation SOP Detectable Level of Change A power analysis is underway to better understand detectable level of change using this protocol Multiple observations by multiple observers and multiple methods are underway at ACAD in order to improve methods dictating replication and sample size 11 Methods Field Season Preparations Prior to the commencement of the field season each year NETN staff communicate with USA NPN NCO staff to obtain any updates to phenophase definitions datasheets or the online interface for the coming season NETN staff provide any relevant updates to participating park staff When possible the NETN Science Communication Specialist updates training materials and hosts an annual training at each participating park during annual park visits Alternatively staff at each participating park or APPA region plan a training session for new and returning volunteers at the start of the fi
300. s OK again Note that if the Olympus ARU is built according to the current design you may be using an adapter and an SD card rather than a microSD card the recorder still refers to this as microSD h Confirm that Mic Sense microphone sensitivity is set to Middle and press OK i Select Finish and press OK 98 SOP 6 Deployment and Maintenance of Autonomous Recording Units 7 Repeat for the second and third recording period for a discrete number of hours using Preset 2 and Preset 3 and setting each to start at the end of the previous preset s 8 hour recording period and end 8 hours after the start time so that one starts right as the previous recording ends 8 Before closing the box confirm that recording begins properly and that the red light turns on 9 Write the file name for the first recording on your datasheet this will be displayed on the screen when the unit is recording 10 Carefully review the ARU Deployment Datasheet filling in any required data Review the checklist items and verify that each item on the checklist has been completed Remember to write all recording start times and SD Card numbers on the datasheet A quick way to make sure the ARU is recording to external memory is to confirm that the countdown timer lists at least 73 hours of record time remaining because this is the maximum file length for files saved to external memory of 4 GB or more using a 128 kbps sample rate
301. s been deployed in a wet or humid environment in the past While the system is moisture resistant water can corrupt the microphones and cause them to output nothing but static or it is possible for the recorder to fail Rectify any issues before proceeding Installation Supplies and Tools Olympus ARU with SD or micro SD card and microphones see SOP 5 4 6 Plastic cable ties 14 long cabletiesplus com item CP 14 120 B 2 Packets of desiccant amazon com item B0038N300Y 4 length of 3 32 vinyl coated steel cable and a 1 8 cable clamp Brass lock with 34 shackle taylorsecurity com item No 4120KA Knife diagonal pliers to trim cable ties 5 16 socket nut driver or adjustable wrench to tighten cable clamp Items listed above without a specified source may be bought at a local hardware store Procedure Select a location with a tree or post that is between 10 cm 4 and 30 cm 12 diameter The tree should have a sturdy branch 1 to 2 m 4 7 above the ground from which to hang the microphone If using a post the microphone may be hung from a cross piece bolted to the vertical post The microphone is placed 2 3 feet from the recorder box to avoid sound blocking distortion Hang the microphone by wrapping the wire over and around the branch several times winding the jack towards the trunk of the tree The microphone may hang any feasible distance from the trunk and should be above deer browse height approx 1 8
302. s program Annual reporting will include descriptive statistics for select phenophases of monitored species Once 10 years of data have been collected network staff can begin to analyze and report on trends in phenology and explore correlations between phenological data and climate variables in order to develop hypotheses about impacts of climate change on phenology Analysis is described in the Data Analysis and Reporting SOP This monitoring protocol requires support from network and park staff and cooperators as well as citizen volunteers Park staff coordinate activities at each participating park including setting up and maintaining designated sites and recruiting volunteers Volunteers interested in making repeat observations attend a training session held annually at each participating park and within each APPA region Training focuses on understanding material in the NETN Phenology Observer Training Manual and includes a brief introduction to phenology locations of designated monitoring sites description of monitored species and phenophases and directions for submitting data online Equipment for observer monitoring is minimal Monitoring via automated sensors requires purchase or construction of autonomous recording units ARUs and cameras memory cards and other equipment xi Acknowledgments This Protocol relies upon the methods datasheets and online infrastructure developed by the USA National Phenology Network USA NPN inc
303. s saved and processed the remainder of the raw data files is discarded Each season park coordinators process audio files using an automated procedure operating within the R statistical environment as described in the Automated Sound Detection and Classification SOP This procedure uses spectrogram cross correlation or binary point matching to detect and classify phenophase status for species of birds frogs and other taxa The resulting processed data set is a time series of phenophase detections Park coordinators may process raw image files using two methods 1 PhenoCam Image Processor PCIP is used to extract red green blue RGB color channel information which can be expressed as an indicator of canopy greenness gcc and 2 flowering and other phenophase information may be manually extracted from image datasets aimed at individual plants Details of both procedures are provided in the Processing Image Data SOP End of Season Procedures In some cases observation may continue year round However for most sites the field season will end in late fall After conclusion of the field season park staff or cooperators will collect automated equipment to be repaired if needed and stored for the winter Site route and individual plant marking is reviewed and replaced if necessary to ensure these exact locations can be found the next year Park staff follow up with volunteers to ensure that all data have been 15 submitted and to solicit fee
304. s will be selected as off points Do this by hovering your mouse over the spectrogram where you want the upper left corner to be and left clicking You will then be prompted to choose the lower right corner of the rectangle Again move your mouse and left click to select the corner All of points within the rectangle will fill with a transparent color if the function call included the default dens 1 the on points will be a solid blue If dens was set to less than 1 the on points will be dotted blue at roughly the density specified You can select multiple rectangles per template to incorporate some areas while leaving out others Right click to end the off point selection process Close the spectrogram window If the selection method is set to auto and no amplitude cutoff value is supplied you will be asked to select a threshold using the h and I raising lowering process When you have pressed Enter twice the entire spectrogram within the specified t lim values and frq lim values will be selected as on and off points at the specified dens proportion The R gui will announce that automatic selection is done Close the spectrogram window The three selection methods the option to either accept the default dens 1 or choose a lower proportion and the option to use a buffer or not means that there are at least 12 different call combinations possible The dens and buffer arguments are continuous so there are really far more than 12 pos
305. scapes plant cams choose photo quality to be WIDE HD 1920 x 1080 or HIGH 2592 x 1944 for TimelapseCam choose MEDIUM 2048 x 1536 for PlantCam Images are saved as JPEG files Image file naming follows this format PARK YYYY MM DD HHMMSS jpg where PARK is the four letter park acronym and is the four digit USA NPN site number YYYY MM DD HHMMSS is the date and time the photo was taken For cameras which do not allow custom file naming such as TimelapseCam images are renamed immediately after downloading using Bulk Rename Utility software as described in Appendix A of SOP 11 Data Management and Quality Assurance Quality Control Maintenance and troubleshooting Plant cams are visited about 1 week after initial deployment to ensure that the camera is still aimed and functioning properly Thereafter plant cams are visited periodically to change batteries and memory cards Rechargeable batteries and memory cards are given unique numbers and labeled with a permanent marker to aid in trouble shooting Maintenance datasheets Appendix S9 A are completed at each visit Webcam IP s are checked at least weekly to ensure that images are updating regularly that the window is not dirty or obscured and that the camera field of view is still as desired e g the housing has not shaken loose Many problems can be fixed simply by temporarily unplugging the ethernet cable to the camera and at the same time cycling the camera s power i
306. se and left click over the desired location You may select multiple vertical and 125 SOP 7 Acoustic Template Creation or horizontal lines on the spectrogram If the default dens 1 value is preserved the lines will appear as purple transects through the spectrogram if dens is set to less than 1 the lines will appear as orange dotted lines at roughly the specified proportion Right click to end the selection process and close the spectrogram window The four selection methods and the option to either accept the default dens 1 or choose a lower proportion means that there are at least eight different call combinations possible The dens argument is continuous so there are really far more than eight possible calls Only a handful of possible calls are demonstrated below In the future you may save your templates and then call them back into R by name so take a few minutes to develop a naming system that works for you Names should be succinct descriptive and unique The database will not allow duplicate names and if you are not using the database duplicate names will create confusion in the future The two parameters you will vary between templates are the FFT parameters and the density so code them into the name if you are not accepting the default If you are also building templates for binary point matching be sure to distinguish between those templates and correlation templates You may use underscores and dashes in the names but do n
307. se images are re named and stored in a separate directory to facilitate identification and subsequent analysis The ColorChecker is not weatherproof and should not be deployed with the camera It is kept indoors in a protective sleeve provided for this purpose and brought out only for camera verification Care must be taken to protect the card from water dirt oils and other sources of degradation Figure S9 2 X Rite ColorChecker Classic card used to verify camera color balance and sensitivity prior to and during field deployment The card is available online for about 70 at B amp H Photo see www bhphotovideo com c product 465286 REG PhenoCam Image Processor PCIP software is used to determine the color as R G and B values of different squares in the ColorChecker card Instructions for downloading and using this software are found in SOP 10 Processing Image Data Alternatively the Macintosh OS utility Digital Color Meter can easily perform this color determination The R G B values 208 SOP 9 Selecting Deploying and Maintaining Automated Digital Cameras for a selection of squares in the ColorChecker are recorded as metadata for each camera as shown here ColorChecker Square Date Row Col Color R G B 8 May 2013 2 2 blue 28 56 140 8 May 2013 2 5 green 170 210 70 8 May 2013 3 4 red 197 10 26 8 May 2013 3 5 pink 208 40 117 To compare two cameras for camera A assume that the blue square in column 2
308. seecccceesecece came Hep d Clicking on the test button will let you know for sure whether you were able to successfully connect to the cloud database If you make it this far you have successfully created an ODBC connection on your Windows machine We ll use this connection to link R to the database importing results into the database This same connection will be used to link Access to the database if you choose to use the Access front end which provides some data entry forms for tables such as tblPerson tblCard tblLocation etc Test Result Ees Connection successful 191 SOP 8 Automated Sound Detection and Classification Appendix S8 B Database Schema QO G i1D_UNIQU n QRO CH F ECKS UNIQUE_C Ha ECKS UNIQUE_CHECKS 0 iD_FOR EIGN_K _KEY_CHECKS QQFOR QRO iD_SQL_MO DE SQL_MODE 1 IGN_K EY CHECKS FOREIGN_KEY_CH SQL_ ODE TRADITIONAL ALLOW_INVALI L Tab le acous tics tblPerson DROP T G ABLE IF ry XISTS acoustics CR F KATE G TABLE I pkP each p as zE ELA PRI ENGINE COMMEN ersonID erson LastName ARY KEY InnoDB T F NOT EXISTS INT NOT NULL AUTO_ This number is automa field serves as the prim
309. sentation of local conditions and uniformity This approach will allow NETN to detect temporal trends in phenological change for key species at these index sites NETN assumes temporal phenological trends at index sites will be indicative of change at other locations within these park habitats However it will not be possible to extrapolate data from these index sites to other locations using this non random sample design This is a significant limitation of the selected sample design but one which is warranted in this case The selected index site design meets NETN sampling objectives to detect temporal change while accommodating the need to monitor conveniently located sites NETN follows USA NPN recommendations for site selection with some modifications as described in the Site Selection and Setup SOP Sites are limited in size to be no larger than a MODIS pixel e g 6 hectares or a 250 m square but will typically be much smaller as described in the SOP At BOHA an island may be considered a single site Frequency and Replication Variability in the timing of phenophase occurrence within individual plants in a population can exceed differences among populations Brugger et al 2003 Goulart et al 2005 However differences in site conditions affecting temperature and exposure altitude slope aspect and nearby development influence phenophase occurrence so we monitor multiple sites at each park At each park at least three
310. sible calls Only a handful of possible calls are demonstrated below In the future you may save your templates and then call them back into R by name so take a few minutes to develop a naming system that works for you Names should be succinct descriptive and unique The database will not allow duplicate names and if you are not using the database duplicate names will create confusion in the future The three parameters you will vary between templates are the FFT parameters the density and the buffer size so code them into the name if you are not accepting the default If you are also building templates for correlation analysis be sure to distinguish between those templates and binary point templates You may use underscores and dashes in the names but do not use spaces slashes colons semi colons periods or commas as they may cause operating system or R errors when written to files 134 SOP 7 Acoustic Template Creation Five non exhaustive example calls to create templates are provided below followed by a sequence of resulting spectrograms Screen captures of some steps are omitted to save space During these calls the R gui will offer prompts such as the ones below for click point selection with the actions initiating the prompt change in italics Interactive amplitude cutoff selection Enter 1 11 11 etc for lower cutoff h hh hhh etc for higher cutoff or hit Enter to continue Current cutoff 51 1 hhhhh Cu
311. signated photopoint sites Analysis is performed using PhenoCam Image Processor a stand alone software program developed by Koen Hufkens In future work we plan to incorporate methods for scaling up to connect this dataset to satellite imagery In addition we are developing procedures to track development of flowering and other phenophases in image datasets List of Key Acronyms DN digital number Zcc green chromatic coordinate PCIP PhenoCam Image Processor software RGB red green and blue ROI region s of interest PhenoCam Image Processor PCIP PhenoCam Image Processor is a stand alone software program built using Matlab functionality PCIP can run on computers without a licensed Matlab copy using Matlab Compiler Runtime MCR provided with the PCIP installer PCIP also called PhenoCam GUI can be downloaded from the website http phenocam sr unh edu webcam tools or obtained from NETN staff To install and run PCIP follow the instructions Installing and Using Phenocam that comes with the software download Selecting regions of interest ROI For tracking seasonal development of greenness in individual plants we select a region of interest within each image dataset comprised almost entirely of leaves of that plant Additional ROIs may be selected for other plants or species represented in the same image dataset For tracking vegetation canopies we select one to three ROIs that are representative of the do
312. sis for each monitored species will include linear regression to determine e Change in selected phenophases over time days year or days decade e Change in selected phenophases per unit of temperature days C or days growing degree day Network staff include phenology reporting within annual Weather and Climate Reports for parks participating in this Phenology Program Annual reporting includes descriptive statistics for 17 select phenophases of monitored species After 10 years of data collection network staff begin analyzing and reporting trends in phenology and explore correlations between phenological data and climate variables in order to develop hypotheses about impacts of climate change on phenology Analysis is described in the Data Analysis and Reporting SOP 18 Personnel Requirements and Training Roles and Responsibilities This monitoring protocol requires support from network and park staff and cooperators as well as volunteer observers At the network level a program leader should provide overall program coordination as well as data analysis and reporting The NETN Science Communication Specialist provides training materials and when possible hosts training sessions during annual park visits The NETN Data Manager obtains network data from the USA NPN database each year Park staff coordinate activities at each participating park including setting up and maintaining designated sites and walking routes and recruiting
313. son takes antibiotics sensitive bacteria are killed but resistant germs may be left to grow and multiply Repeated and improper uses of antibiotics are primary causes of the increase in drug resistant bacteria e Misuse of antibiotics jeopardizes the usefulness of essential drugs Decreasing inappropriate antibiotic use is the best way to control resistance e Antibiotic resistance can cause significant danger and suffering for people who have common infections that once were easily treatable with antibiotics When antibiotics fail to work the consequences are longer lasting illnesses more doctor visits or extended hospital stays and the need for more expensive and toxic medications More information on Lyme Disease and Ticks Center for Disease Control http www cdc gov lyme also a free webinar on tickborne diseases American Lyme Disease Foundation http www aldf com Tick Management Handbook http www ct gov caes lib caes documents publications bulletins b1010 pdf 44 SOP 1 Safety Poisonous Plants and Animals Both for safety and protection of park resources it is never advisable for monitoring staff to eat wild plants while working in a National Park regardless of their confidence in plant identification Keep a safe distance from wildlife Poison Ivy Poison ivy Toxicodendron spp is present in most NETN parks and can be very abundant in localized areas When working in areas with poison ivy it is advis
314. space and enough permanent hard drive storage available for the resulting data For bats and migrating birds recording does not need to be continuous if data processing and storage are a significant concern However until specific data on detection rates is available recording for at least 10 minutes per hour between dusk and dawn is recommended As Figure S6 6b shows if recording for only 10 minutes per hour D cell batteries may be sufficient to power SM units However for continuous recording an external deep cell battery is recommended Figure S6 6 illustrates the tradeoffs between sampling rate and power and memory capacity WACO is the lossless compression format offered by Wildlife acoustics in the SM1 and SM2 ARUs The SM2 has additional lossy compression options available that are described in the user s manual but are not recommended at this time Test The Unit A few weeks before taking the unit into the field insert a memory card and make a test recording Download the recording and verify that the unit is working as it should and is not recording distorted files or files full of static This is especially important if a unit has been deployed in a wet or humid environment in the past While the system is moisture resistant 102 SOP 6 Deployment and Maintenance of Autonomous Recording Units water can corrupt the microphones and cause them to output nothing but static or it is possible for the recorder to fail Rectify
315. span a frequency band gt kHz and have durations gt 1 second Vocalizations with durations lt 1 second might benefit from increased time resolution which is achieved with smaller window lengths lt 512 Vocalizations that span lt 1kHz may benefit from more frequency resolution which is achieved with longer window lengths gt 512 Increasing the overlap for longer window lengths allows some time resolution to be returned Overlap is specified as percents ranging from 0 to 99 typical values are 0 50 75 and 95 Specifying new FFT parameters in the template will pass the parameters to the survey as well The process of making a binary point template will follow these general steps Call the function specify the wav clip to use identify the start and end of it in seconds and the frequency limits in kHz identify the selection method choose either click rect or auto and identify how dense the points within the template will be with the click selection method use the default of dens 1 and the default of binary FALSE for other methods choose binary TRUE and if dens 1 all points within the selection area will be saved and for dens less than 1 only the specified proportion of points will be chosen Dens 0 2 will save roughly every fifth point dens 0 5 will save roughly every other point etc The binary template has the option to include a buffer around signal points if the buffer 0 off points will be se
316. ss choose Stop if prompted Close the spectrogram window If the selection method is set to rect or rectangle you will be prompted to select the upper left corner of the rectangle Do this by hovering your mouse over the spectrogram where you want the upper left corner to be and left clicking left click and release You will then be prompted to choose the lower right corner of the rectangle Again move your mouse and left click to select the corner A colored rectangle will fill the area between the two clicks if the function call included the default dens 1 the rectangle will be a solid purple If dens was set to less than 1 the rectangle will be dotted orange at roughly the density specified You can select multiple rectangles per template to incorporate some areas while leaving out others Right click to end the selection process Close the spectrogram window If the selection method is set to auto the entire spectrogram within the specified t lim values and frq lim values will be selected at the specified dens proportion The R gui will announce that automatic selection is done Close the spectrogram window If the selection method is set to line you will be prompted to choose either the upper or left start point of the line Do this by hovering your mouse over the spectrogram and left clicking at the desired location Now you will be prompted to choose the lower or right point of the line Again move your mou
317. sure that fatigue does not become a factor Environment Environment was assigned a low score 3 because the work may involve some travel off of established trails on uneven terrain Activities may occur during a variety of weather conditions although staff are told not to monitor if the weather forecast calls for severe weather Incident Complexity Incident complexity was assigned a medium score 5 because daily field conditions change due to weather Individual monitoring staff must use judgment and experience to respond appropriately Step 5 Evaluate Risk vs Gain The scores for this assessment fall near the top of the green zone indicating a low risk activity While it is theoretically possible to make changes to reduce risk even further doing so will likely cause volunteers to leave the program due to intrusive requirements The NETN Program Manager feels that the current procedures provide a good balance that encourages monitoring 53 SOP 1 Safety Appendix S1 A Green Amber Red Risk Assessment continued staff to be safe without being overly protective NETN feels that this monitoring activity if carried out in accordance with all SOPs has an acceptable level of risk Step 6 Execute Decision The decision made by the NETN Program Manager is to conduct the activity in accordance with NETN Phenology Monitoring Protocol Standard Operating Procedures SOPs Step 7 Supervise Watch for Change The NETN Progra
318. t jack as seen above The Pelican case is watertight but the input jack is still exposed Open the case place two desiccant packs inside and verify that the unit can power up Set Up Continuous Recording The Olympus ARU does not have the recording flexibility of the Wildlife Acoustics Song Meter the Olympus is limited to three pre set recording intervals per day For this reason our recommended procedure is to set the Olympus ARUs for continuous recording with a new audio file produced every 8 hours We will then subsample this data stream for 5 minutes per hour Only the subsampled data will be analyzed and archived In order to facilitate file renaming preset recording intervals for the Olympus ARU must be a discrete number of hours 1 e x hours and 0 minutes The Olympus DM 420 records MP3 and WMA files with several possible qualities the MP3 option with the lowest quality 128 kbps option is recommended regardless of sampling schedule Use the following procedure to set up and initiate recording 1 Turn on the recorder by sliding the on button behind the stop button down and holding for a few seconds 97 2 3 4 5 6 SOP 6 Deployment and Maintenance of Autonomous Recording Units If not done ahead of time set the time and date as close as possible to the official US time at http www time gov timezone cgi Eastern d 5 java Set the unit to 24 Hour time while in the time and date menu by pressing th
319. t property is damaged fatality occurs medical treatment is required and or a reasonable possibility of a tort claim is expected 48 SOP 1 Safety 3 Thefts and Vandalism should be reported to Park Law Enforcement Officials rather than reported on SF 91 4 Reporting Multiple Vehicle Accidents when a privately owned vehicle damages Government property two reports SF 91 are required one report for the Government property and one for the private operator 49 SOP 1 Safety Appendix S1 A Green Amber Red Risk Assessment This appendix describes application of the GREEN AMBER RED GAR Risk Assessment Model as outlined in the NPS Operational Leadership Student Manual Version 2 July 2011 to the NETN Phenology Monitoring Protocol This GAR was written by the NETN Program Manager Brian Mitchell on 26 February 2012 revised based on internal review on 11 November 2012 and approved by the NPS Northeast Region I amp M Program Manager John Karish on 9 May 2013 The GAR model allows for a general assessment of a task or operation and generates communication concerning the risks of an activity in this case conducting the field based activities of the NETN Phenology Monitoring Protocol The most important part of the process is the team discussions leading to an understanding of the risks and how they will be managed The GAR is a seven step process Each step is defined and explained in the context of the NETN Phenology Moni
320. t the recorder to make several long files each day and then extract short surveys from those longer recordings Package monitoR has a function that calls the software mp3splt which can be downloaded from http mp3splt sourceforge net mp3splt_page home php Installation options are available for any operating system An advantage to this software is that it does not decode and re encode the mp3 files to split them so no audio quality is sacrificed A package is a set of functions that runs in R 158 SOP 8 Automated Sound Detection and Classification Terminology Bandpass filter An audio filter that trims frequency data from above and below the frequency band that is allowed to pass through In the digital implementation here we specify a minimum and maximum frequency that we want to pass through and all frequencies below the minimum and above the maximum are discarded Binary point matching A method for sound detection in which the acoustic template is converted to a matrix of on and off cells The mean amplitude in decibels of the corresponding on points at each time interval in the survey is compared to the mean amplitude of the corresponding off points The user specifies a minimum acceptable difference between the two values to limit the results and local maximum difference values above the minimum value identify events MP3 A lossy compression file format engineered to preserve the
321. ta rich it provides information on presence absence and duration of phenophases Another advantage of status monitoring is that is typically easier for citizen volunteers to interpret and record than whether or not a phenological event has occurred At each participating park at least three sites are selected for phenology monitoring within each monitored habitat Due to the reliance on volunteer monitors and the high sampling frequency needed for phenological observation sites are selected for convenience of access and presence of monitored species in addition to lack of human disturbance representation of local conditions and uniformity This approach will allow NETN to detect temporal trends in phenological change for key species at these index sites NETN assumes temporal phenological trends at index sites will be indicative of change at other locations within these park habitats The selected index site design meets NETN sampling objectives to detect temporal change while accommodating the need to monitor conveniently located sites Following USA NPN recommendations NETN observers are instructed to monitor sites at least weekly but ideally every other day when phenology is changing quickly such as in the spring and fall At most sites data from multiple observers is pooled to achieve optimum frequency This approach balances the need for frequent observations with the recognition that volunteer monitors may not be able to pa
322. tblProgram tbProject tblPriors DESCRIPTION Stores information about memory cards Tracks which surveys are recorded by which recorders Stores information about recording units Stores information about all locations in the project Stores attributes of the survey recording Stores information about all types of templates used in the project Stores the results of findPeaks Stores information about the target species For archiving sound clips extracted from surveys Stores the names of people involved in the monitoring project Stores contact information for all people in tblPeople Identifies the primary investigative organization Stores the names of monitoring programs of each organization Stores names of monitoring projects in each program Stores priors for Bayesian updating 160 SOP 8 Automated Sound Detection and Classification File management The process of retrieving and analyzing environmental acoustic data involves a large number of audio files this SOP describes a system for managing and organizing these files Set up the following file directories on your storage drive You will need these directories regardless of whether you use a database e A main folder called Acoustics e Nested within Acoustics are six folders o Recordings for temporarily holding files that are not wav or mp3 files such as Wildlife Acoustics wac files Surveys for holding files that are ready for analysis including wav or mp3
323. ted for phenology monitoring Tables 1 and 2 The list of key species will be updated periodically as new information becomes available or management focus changes See Appendix A for monitored phenophases Table 1 Plant species selected for phenology monitoring in NETN designated park habitats Core habitats and associated species are shown in bold The two core habitats are widespread and ecologically important within most NETN parks Plant species Garlic mustard Alliaria petiolata White wood aster Eurybia divaricata Red maple Acer rubrum Sugar maple Acer saccharum Marsh marigold Caltha palustris Purple loosestrife Lythrum salicaria Bunchberry Cornus canadensis Painted trillium Trillium undulatum Hobblebush Viburnum lantanoides Balsam fir Abies balsamea Common milkweed Asclepias syriaca Rough stemmed goldenrod Solidago rugosa Beach pea Lathyrus japonicus Beach rose Rosa rugosa Rockweed Ascophyllum nodosum Lifeform Forb herb Forb herb Broadleaf tree or shrub Broadleaf tree or shrub Forb herb Forb herb Forb sub shrub Forb herb Forb herb Conifer Forb herb Forb herb Forb herbaceous vine Broadleaf tree or shrub Seaweed Designated habitat Northern hardwood forest Northern hardwood forest Northern hardwood forest Permanent freshwater wetland Northern hardwood forest Permanent freshwater wetland Permanent freshwate
324. than across the rows The columns can also be summarized in R using something like colMeans colMeans compSscores na rm TRUE and max colMeans comp scores na rm TRUE After doing this I see that s10 has the highest mean correlation with all other song examples Here is the resulting matrix 151 sl s2 s3 s4 3 2 1 000 0 706 0 573 0 565 8 8 0 709 0 912 0 636 0 622 15 0 0 571 0 613 0 869 0 620 21 7 0 606 0 602 0 633 0 999 27 8 0 703 0 785 0 600 0 597 33 7 0 629 0 675 0 633 0 640 39 0 0 617 0 648 0 547 0 548 45 0 0 610 0 637 0 591 0 628 51 0 0 599 0 651 0 656 0 597 57 6 0 684 0 751 0 713 0 670 63 4 0 634 0 705 0 729 0 650 69 1 0 696 0 809 0 610 0 612 75 3 0 587 0 594 0 573 0 530 80 6 0 684 0 797 0 644 0 614 86 2 0 633 0 673 0 544 0 549 92 1 0 599 0 623 0 586 0 617 97 3 0 605 0 631 0 510 0 525 03 3 9 697 0 802 0 632 0 601 08 8 0 649 0 704 0 524 0 525 14 9 0 666 0 744 0 660 0 622 20 4 0 636 0 698 0 563 0 568 26 1 0 670 0 756 0 581 0 557 31 8 0 638 0 720 0 567 0 607 TSI gt colMeans comp scores na rm TRUE sl s2 s3 s4 s5 0 657 0 706 0 616 0 611 0 697 gt max colMeans comp scores na rm TRUE 1 0 715 s5 0 717 0 787 0 590 0 592 0 897 0 640 0 696 0 616 0 627 0 750 0 681 0 791 0 585 0 744 0 680 0 630 0 636 0 815 0 723 NA 0 673 0 756 0 716 s6 0 653 s6 0 626 0 683 0 625 0 631 0 648 0 948 0 594 0 641 0 643 0 737 0 687 0 679 0 602 0 658 0 624 0 633 0 581 0 649
325. the PA3 microphone for its exceptional noise floor use of this optional microphone may require some adjustment to the procedures below Use of the PA3 microphones will also require an RCA to 3 5mm stereo plug adapter about 5 and will save on some soldering work Usually sold as a full roll rather than as bulk wire but only 4 10 is used in one recorder see note in microphone construction section 3 Optional purchase for media storage if microSD cards are undesirable or unavailable 82 SOP 5 Building an Autonomous Recording Unit Additional Equipment to Purchase Locally 6 18 gauge black wire 6 18 gauge red wire 2x 3 8 dowel cut to 1 5 8 length 1 brass thumb tack 1 brass screw 4 x 14 8 screws 6 x 14 Solder 3 deck screws 1 1 4 3x 4 cable ties Waterproof glue 7 x 4 5 board of Lauan or similar 4 lightweight plywood oak or birch are more eco friendly than lauan MDF HDF or Homosote are not recommended due to moisture exposure 5 length of 2 x2 wood 7 32 steel rod cut to 6 length Heat shrink tubing or electrical tape 28 of 1 wide double sided Velcro strap 8 plastic dish 4 wire mesh or hardware cloth 6 5 x 10 5 Faux fur Tools Required Soldering iron Diagonal pliers Needle nose pliers Wire stripper Phillips 2 screwdriver Electric drill 7 32 Drill bit 5 32 Drill bit 1 8 Drill bit 1 16 Drill bit Swagin
326. these perhaps the best known is the Wildlife Acoustics Song Scope platform which uses a Hidden Markov Model algorithm with carefully developed recognizers to detect species on field recordings After much consideration we decided not to use Song Scope for the following reasons 1 Song Scope is a black box and it is not clear exactly what the recognition algorithm does 2 Song Scope recognizers can only be built by many rounds of trial and error and tweaking numerous parameters Building recognizers is an art not a science 3 Song Scope is not suitable for long term monitoring since regular software updates alter the recognition algorithm and require complete reanalysis of all prior data to ensure consistency 4 Song Scope is expensive especially for a program intended to run in a distributed fashion with many people running analyses NETN staff and cooperators decided that the best approach would be to use simple algorithms spectral cross correlation and binary point matching While these algorithms are perhaps not as accurate as the latest software they are easy to explain and visualize have many fewer parameters to worry about when trying to build templates and have been shown to be accurate for identifying many species The approach can also be implemented on a free widely used platform R and because the basic algorithms are not being changed over time old data does not need to be reanalyzed unless a new species tem
327. ticipating parks Visitors are invited to review USA NPN phenophase descriptions and instructions and to make observations on marked individual plants Participants record observations on Nature s Notebook datasheets provided onsite and subsequently submit observations online in Nature s Notebook Monitors making repeat observations first attend a 1 to 3 hour training session as described in the Observer Recruitment and Training SOP The training includes a description of monitored habitats and specific monitoring sites available at that park a list of plant and animal species available for monitoring at that park and guidance on making observations The NETN Phenology Observer Training Manual provides user friendly instructions for volunteer monitors Trained monitors visit their site s at least once per week but ideally every other day during periods of rapid phenological change such as in the spring or fall Observations can be made at any time of day but monitors are encouraged to visits sites consistently around the same time of day This is because some animal species tend to be more active at certain times of day and plant activity can vary over the course of the day 77 To monitor plants one to three marked individuals of each monitored plant species are observed during each visit Observing three individuals at each site is best for understanding how phenology varies among individuals at a site but data from only one or two indi
328. tional historic sites in the Northeastern United States This protocol was developed in collaboration with and relies upon the procedures and infrastructure of the USA National Phenology Network USA NPN including Nature s Notebook USA NPN s online plant and animal phenology observation program www nn usanpn org Organized in 2007 USA NPN is a nation wide partnership among federal agencies schools and universities citizen volunteers and others to monitor and understand the influence of seasonal cycles on the nation s biological resources The overall goal of NETN s phenology monitoring program is to determine trends in the phenology of key species in order to assist park managers with the detection and mitigation of the effects of climate change on park resources An additional programmatic goal is to interest and educate park visitors and staff as well as a cadre of volunteer monitors Specific monitoring objectives of this protocol are to e Develop and maintain a list of key species that are of scientific or management interest and are suitable for phenology monitoring within NETN parks e Detect long term trend in timing and abundance of monitored phenophases of key species at index sites in designated core and optional park habitats e Explore correlations between phenological data and climate variables including mean monthly temperature and degree days in order to develop hypotheses about impacts of climate change on phe
329. tions and 3 automated sensors digital cameras and audio recorders are used to record data at select locations In addition to collecting data at an optimal frequency automated sensors can be used at difficult to access or sensitive sites or can provide a useful quality control check when used in conjunction with volunteer observations The data collected using this protocol will support the interpretation of several other NETN Vital Sign monitoring programs Mitchell et al 2006 Breeding Birds migration and breeding phenological data will inform monitoring of population sizes such as when to monitor how to interpret changes in number of individuals observed potential causes of changes in abundance and changes in habitat relationships Early Detection of Invasive Species phenological data will inform timing of management actions and aid in identification of species most likely to become invasive in the future Amphibians and Reptiles phenology can be incorporated into monitoring of amphibian population sizes and can identify potential threats to amphibians Climate phenology provides a biological indicator of change that integrates several climate variables in ways that are biologically meaningful Sampling Design Approach NETN trains and supports volunteer monitors and uses automatic recording devices to collect phenological data as described herein Using volunteers provides the dual benefit of engaging the
330. tive and may be revised to lower frequencies or shorter durations if research indicates this is warranted If both birds and anurans are of interest use the higher sampling rate 24 kHz Table S6 1 Recommended sampling rate and schedule by taxon and monitoring purpose Taxon Purpose Sample Rate Schedule Notes Anurans Breeding Season 16 kHz 10 min hour Omnidirectional mic Birds Breeding Season 24 kHz 10 min hour Omnidirectional mic Birds Migration Season 24 kHz Continuous one hour before Directional mic aimed dusk to one hour after dawn at sky Continuous one hour before Ultrasonic Pats Feeding aus dusk to one hour after dawn omnidirectional mic Audio files may be subsampled after collection to yield standardized 5 min hr samples for analysis The appropriate sample rate depends on the frequency of the calls being recorded At a minimum the sample rate must be twice as high as the vocalization frequency used by the species being recorded and in practice the sample rate should be somewhat higher approximately 2 5 times the vocalization frequency is a good rule of thumb For example if you are recording high pitched warblers such as the Blackburnian Warbler you will need to record at a minimum sampling rate of 22 05 kHz to capture the high frequency trills above 8 kHz See Table S6 1 for specific recommendations Recording more frequently or at higher sample rates is optional if there is sufficient battery power and memory card
331. toring Protocol below Step 1 Define the Mission or Task The NETN Phenology Monitoring Protocol includes a field based monitoring activity surveying the phenology of plants and animals at different sites or along routes in different habitats Monitoring staff are usually volunteers who work independently and are coordinated by the park Natural Resource Program Manager Staff are encouraged to work in pairs if visiting remote or hard to access locations and NPS has agreed to help find partners for monitoring volunteers when the volunteers request a partner The activity is sometimes conducted away from roads and trails Potential safety hazards along with mitigation measures have been identified in a Job Safety Analysis JSA Appendix B Of specific concern is that monitoring staff may be working in fairly remote areas with limited communication options in the event of an emergency especially at ACAD and APPA A serious injury due to a trip and or fall while traversing uneven or steep terrain is possible and is the most significant risk encountered when conducting this activity Step 2 Define the Threats The threats hazards for this activity along with mitigation measures are described in the associated JSA Appendix B Step 3 Assess Risk and Assign a Numerical Value The numerical ranks Table 1 1 were assigned by Brian Mitchell the NETN Program Manager and the NPS project leader for the NETN Phenology Monitoring Protocol NPS staff re
332. troduction to phenology and this program Location of designated monitoring sites and description of site marking at that park Plants and animals to observe at that park How to choose and mark plants if allowed at that park How to create an online account in Nature s Notebook How and when to make observations How to record and submit data A complete example of making phenology observation A chance to ask questions Online Training Materials Useful online training materials are available on USA NPN s Nature s Notebook website www usanpn org nn training videos The following topics are presented online both as PowerPoint presentations and as training videos e Record plant observations e Record animal observations e Enter plant observations online e Enter animal observations online Additional training materials available on this website are not used as part of this program because procedures in our parks differ from general USA NPN instructions It is important that park coordinators stress to all observers that within national parks monitoring only occurs at designated sites and that any marking of individual plants if allowed strictly follows rules for marking at that particular park In this program observers choose among species selected for monitoring at that park Feedback Observers are surveyed annually to assess satisfaction and solicit suggestions for improving the program including training and data
333. ts x x Xx 250 SOP 12 Data Analysis and Reporting Appendix 12 A Selected Phenophases for NETN Species continued Table S12 A 6 Monitored phenophases for birds Red White Great PrapreseOvembtd Bobol winged Wrap ented Tron pach Active individuals x x xX xX xX x x Feeding x x x x x x x eae E Z 4 x Insect consumption X x x x x Flower visitation Nut gathering Calls or song x xX x xX x x x Singing males x xX xX x x Mating x x x x x x Nest building X xX x x xX Dead individuals x x x x Xx x Individuals at a X e x x X feeding station Table S12 A 7 Monitored phenophases for Insects Lepidoptera USA NPN Phenophase eatetcillat butiefiy Active adults x x Flower visitation x Migrating adults x Mating x x Active caterpillars xX x Caterpillars in tent x Caterpillars feeding x X Dead caterpillars x x Dead adults x x Individuals at a feeding station x Individuals at a light x Individuals in a net x x 251 SOP 13 Protocol Revision Northeast Temperate Network Version 1 02 Overview This SOP outlines the procedures and deadlines for making changes to the phenology protocol Revision Process NETN staff and cooperators involved in this protocol will teleconference or meet annually in the late fall or early winter to review the prior season s work Ideally staff from each participating park and organization including the Appalachian Trail Conservancy will participate to convey
334. ture Search F Insert amp Empty Drop 12 Xeround lalint_swedish_ci unknown T tibevent tibevent T Browse Structure amp Search 3e Insert GF Empty Drop 12 Xeround latini_swedish_ci unknown Create table 13 tables Sum 156 Xeround latint_swedish_ci oB on t__ Check All Uncheck Ail With selected amp Print view g Data Dictionary A Create table For example here is the Structure of tblPerson showing the four fields that make up this table pkPersonID fldFirstName fldMiddleName fldLastName The structure indicates that the pkPersonID is the primary key for this table and that it is set to AUTO_INCREMENT this means the database will assign an ID for any new entry 188 SOP 8 Automated Sound Detection and Classification Appendix S8 A Creating a MySQL database continued _ Browse Structure SQL 4 Search 4i insert Export j Import Operations Triggers Name Type Collation Attributes Null Default Extra Action 1 pkPersoniD int 11 No None AUTO_INCREMENT f Change Drop F Browse distinct values g Primary g Unique w More 2 fidFirstName varchar 45 latin1_swedish_ci No None amp Change Drop Browse distinct values Primary y Unique w More 3 fldMiddleName varchar 45 latin1_swedish_ci Yes NULL Change Drop _ Browse distinct values _ Primary _y Unique w More 4 fildLastName varchar 45 latin1_swedish_ci No None amp Change Drop _ Browse distinct values Prima
335. udit MABI_1234_2012_10_10_033521 txt sa EPMT 2010 zi gt M Reg Expr 1 R Replace 3 R Removals a Bh Auto Date 7 lu 9 R Match Replace Fistnchars fo 4 Prefix MAB1123 j Lastnchas 0o Type Modified gt Replace Insert Fmt Custom x From fo tofo a ae at pos Sep Sega Custom _ Y_ m_ d i P Words Sut I Cent off Fa Name Remove gt T Digits Chars Append Folder Name 8 F Symbols I High Name None J Sepsa M Selections 11 7 Fades Hidden Bh New Location 123 prj Prec IZ Fies I Recursive Pa c 1 Objects 1 Selected fTest_Template 7 INSTRUCTIONS 1 Before starting make a copy of all the files you will be renaming 2 Navigate to the folder containing the copies of the files you wish to rename 3 Using the selection windows select the file s you wish to rename SHFT or CTRL click to select more than one 4 Set Filename to Remove 5 Add the 4 letter park acronym and 4 digit site code assigned by USA NPN e g MABI1234 6 Add an autodate Date should be added as a suffix Type Modified uses the modified date stored in the file s properties Format Custom For image files use this custom date format Y m_ d H M S OR For audio files use this custom date format Y m d_ H M S e For Olympus audio files offset subtract the length of the recording in hours 7 Verify for
336. ues to a low value of 0 34 below the baseline Leaf abscission then exposes the grayish tree trunks which returns gce to its normal baseline of 0 36 In addition analysis of red chromatic coordinate rec may be used to quantify autumn coloration 219 SOP 10 Processing Image Data Harvard Forest 2009 0 4 GCC RCC oO oh 0 3 green up senescence 0 2 50 100 150 200 250 300 350 Day of Year Figure 10 2 9 rcc time series from a Harvard Forest webcam in 2009 The seasonality of greenness at evergreen dominated forest sites in the northeast US is largely controlled by seasonal changes in chlorophyll and pigment composition of existing foliage rather than growth and senescence of new leaves Thus NETN evergreen dominated sites are expected to show a slightly different but still distinct phenology of change in greenness Analysis of phenophases for cameras aimed at individual plants These procedures are a first draft they will be refined as camera data is collected and personnel become available to analyze the image data For plants that have stable areas suitable for automated analysis of gcc primarily trees and shrubs with stable branches the procedures described above should be used to automatically extract this information For other phenophases the photos will be reviewed and the phenophases for each day with suitable photography will be recorded in Nature s Notebook It will help to use a computer with two
337. ule and battery and media capacity see SOP 6 Install the recorders see SOP 6 Perform battery and media refreshes at established intervals see SOP 6 Convert recordings to wav format herein Locate suitable template songs in the survey recordings or record them with a directional microphone or purchase them from the McCaulay Library of Natural Sounds discuss with NETN procedures outlined in SOP 7 Acoustic Template Creation 10 Use the R package to convert recordings to environmental data herein 11 Save csv files or upload results to the database or both herein 12 Archive the surveys or events herein 13 Optional Human observer verifies the results discuss with NETN herein eo ONS Software Programs Used Sound detection is performed within R a freely available language and environment for statistical computing and graphics which can be downloaded from the Comprehensive R Archive Network http cran r project org Before using R for spectrogram cross correlation or binary point matching add these packages to your R library 1 tuneR 2 plyr 3 RODBC for connecting R to a database 4 seewave optional for displaying spectrograms in R has dependencies rgl rpanel fftw see http rug mnhn fr seewave inst html for solutions to known installation issues See Appendix S8 C for instructions on downloading R and selected packages If recording mp3 files it is sometimes necessary to se
338. umber of Samples 14571815 Duration seconds 607 16 Samplingrate Hertz 24000 169 SOP 8 Automated Sound Detection and Classification Channels Mono Stereo Mono Bit 8 16 24 32 16 Template information 4 binary templates original recording BINWd1 0BIN C Users jkatz3 Dropbox LabDemo Templates BTNW wav BTNWpoint1 0BIN C Users jkatz3 Dropbox LabDemo Templates BINW wav BINWd 8BIN C Users jkatz3 Dropbox LabDemo Templates BTNW wav BTNWauto 5BIN C Users jkatz3 Dropbox LabDemo Templates BTNW wav lower frequency upper frequency duration on points off points BTNWd1 O0BIN 3 562500 6 703125 2 239 735 6282 BTNWpointl OBIN 2 671875 8 156250 231 25 73 BTINWd 8BIN 3 515625 6 609375 2 47 192 1756 BTNWauto 5BIN 2 015625 8 953125 2 77 192 4566 score cutoff BTNWd1 0OBIN 9 BTNWpoint1l OBIN 9 BTNWd 8BIN 9 BTNWauto 5BIN 9 Score information min score max score n scores BTNWd1 0OBIN 8 44 28 75 28348 BINWpoint1 0OBIN 8 85 39 17 28349 BINWd 8BIN 9 46 28 62 28344 BTNWauto 5BIN 7 62 30 49 28330 The list of scores is probably very long as there will be one record for each time bin minus the template length The next step is to identify events within the score list and specify a cutoff threshold which is done with the findPeaks function Event analysis The function findPeaks identifies events within the correlation and binary point match scores and returns a list of event times and pea
339. uneR readWave and adjust the sampling rate using monitoR changeSampRate You will need to save the track again tuneR writeWave for the changes to be saved To check or change the sampling rate in R load the tuneR package from your library and assign your template to an object within R using the readWave command BINW lt readWave C Users jkatz3 Dropbox LabDemo Templates BINW wav Check the sample rate by viewing the details of your new object BINW Wave Object Number of Samples 68212 Duration seconds 2 84 Samplingrate Hertz 24000 Channels Mono Stereo Mono Bit 8 16 24 32 16 Change the sampling rate using the changeSampRate command which spline fits new sample values and can thus upsample BINW lt changeSampRate BTNW sr new 44100 In tests conducted using synthesized and actual recordings the changeSampRate function did not produce aliasing artifacts or other noticeable problems in spectrograms However these tests were limited and spectrograms should be spot checked after resampling to ensure that they closely match spectrograms from the original recording If your template is listed as Stereo you may opt to make it mono using tuneR s channel function Choosing a single channel will save memory as it is loaded into R plus it will reduce ambiguity if the signal in the two channels differs 123 SOP 7 Acoustic Template Creation BTNW lt channel BTNW which c left Substitute right for
340. unit In Service Needs Repair or Recycled no longer an asset of the program De g fldSerialNumber VARCHAR 45 NULL COMMENT The manufacturer s serial number of the unit fldComments VARCHAR 45 NULL COMMENT Comments about the unit as PRIMARY KEY pkRecorderID InnoDB COMMENT This table stores information about recording units CREATE UNIQUE INDEX pkRecorderID_UNIQUE ON acoustics tblRecorder pkRecorderID ASC Table acoustics tblCard DROP TABLE IF EXISTS acoustics tblCard CREATE TABLE IF NOT EXISTS acoustics tblCard pkCardID INT NOT NULL AUTO_INCREMENT COMMENT This field assigns a unique number to each SD card used in the monitoring program This number is 194 SOP 8 Automated Sound Detection and Classification Appendix S8 B Database Schema continued automatically assigned and the field serves as the primary key for this table fldManufacturer VARCHAR 45 NULL COMMENT The manufacturer of the card e g Sandisk fldStorageSize INT NULL COMMENT This is the size of the card in GB For example 256 is a 256 GB card fldDatePurchased DATE NULL COMMENT The date the card was purchased fldStatus ENUM Active Failed NULL COMMENT The status of the card Active or Failed
341. ure s Notebook at www nn usanpn org Nature s Notebook is an online plant and animal phenology observation program of the USA National Phenology Network Most designated sites in NETN parks are shared sites for which multiple 68 SOP 2 Site Selection and Set Up observers submit data Note that a shared site is different from a public site a site at which anyone could register and submit data observations Shared sites are administered by park coordinators in coordination with USA NPN and are accessed by a discrete set of trained observers Alternatively any site at which informational displays are used to attract park visitors to make one time or initial observations must be registered as a public site to enable any visitor to submit an observation for that site into Nature s Notebook To begin the park coordinator registers a new partner group with USA NPN NCO staff by emailing nco usanpn org with the name of the network NETN the park ie ACAD and a list of existing users who will submit observations at this park Once the group is established the park coordinator adds shared sites and monitored plants online These sites and plants are accessible online by all members of the group New monitors join the group online by choosing Edit from their Nature s Notebook account homepage then selecting a park group from the list of partner organizations To do this first choose National Park Service as th
342. ver data Accessing Environmental Data Weather data for NETN parks is compiled and reported in annual Weather and Climate reports Weather data are obtained by the NETN data manager from the NPS enterprise weather database in Fort Collins CO these data are compiled from weather stations within or Managed by Brent Frakes 245 SOP 12 Data Analysis and Reporting surrounding the parks To better understand conditions within each park gridded Parameter elevation Regressions on Independent Slopes Model PRISM data and Drought Monitor data are obtained from associated internet portals and analyzed for park specific locations as described in the NETN Weather and Climate reports Data validation During annual training park coordinators assign a skill classification to each observer This classification provides a rough measure of confidence in the observer s abilities using a 3 point scale beginner typical or expert the middle value typical is considered the default rating Unusual observations from observers rated as beginner or from untrained observers may be removed from analysis The dataset obtained from USA NPN identifies observers by an identification number assigned by USA NPN rather than observer name for compliance with the Privacy Act Thus in order to consider observer skill level in this analysis park coordinators or NETN staff may need to provide USA NPN with a list of trained observers with each class
343. veral seconds to each pass Combining the templates will also expedite saving them for future use either locally or in a database The combineBinTemplates function is demonstrated below This process assigns a default score cutoff to all templates For binary point matching the score is the difference between the mean amplitude of the on points and the mean amplitude of the off points the score units are decibels dB This call assigns a default score cutoff for all templates Gather templates into a list BINtemplates lt combineBinTemplates BT TNW_rect_d100_b2_B TNW_rect_d20_b2_B W d WWW B NW_rect_d100_B TNW_auto_d80_b2_B iss one Use th INtemplates lt combi same function to add it to the list neBinTemplates BINtemplaets BTNW_click_d100_B Speci fy a new score cutoff for ach template individually INtemplates lt BINtempl BT templateCutoff ates NW_rect_d100_B 9 TNW_rect_d100_b2_B 8 5 score cutoff c TNW_rect_d20_b2_B 9 5 TNW_auto_d80_b2_B 8 5 w w w w TNW_c Lick_d100_B 7 Rename them too INtemplates lt temp lateNames BINtemplates c vector of names 146 SOP 7 Acoustic Template Creation The print method for this class returns a summary of all templates in the list when called gt BINtemplates Object of class binTemplateList containing 5 templates original recording
344. viduals is useful as well Each individual plant is observed for each phenophase during a visit and data is recorded on Nature s Notebook datasheets For most plant phenophases observers also check and report on phenophase intensity or abundance like the number of flowers or percentage of open flowers seen Phenophase abundance choices are described on Nature s Notebook Phenophase Definition sheets for each species Observers are encouraged to use binoculars to see phenophases in tall trees Herbaceous plants growing in clumps may be monitored as a patch rather than an individual Setup a patch as directed in the Site Selection and Setup SOP and make sure to properly designate the patch in Nature s Notebook by clicking the check box for Patch when registering the plant and report patch size Evaluate the phenophases in the patch as if all of the stems in the patch are a single individual If an individual plant dies or is obviously declining in health when others of the same species around it are still healthy park staff choose a new individual as described in the Site Selection and Setup SOP and report the death of the previous individual Never substitute observations from a nearby healthy individual when a marked plant is missing dead or declining Instead mark and register the new individual plant and report observations for the new monitored plant To observe animals monitors look and listen for the species on the
345. viewed the ratings and analysis and their suggestions were incorporated It should be noted that at the time numerical values were assigned February 26 2012 the protocol had been in development for 4 years and similar protocols had been in place for up to 6 years and considerable time and effort had already gone into evaluating and mitigating risks The GAR process is described in NPS Operational Leadership Student Manual Version 2 July 2011 The activity risk can be visualized using the colors of a traffic light If the total risk value falls in the GREEN ZONE 1 35 risk is rated as low If the total risk value falls in the AMBER ZONE 36 60 risk is moderate and you should consider adopting procedures to minimize the 51 SOP 1 Safety Appendix S1 A Green Amber Red Risk Assessment continued risk If the total value falls in the RED ZONE 61 80 you should implement measures to reduce the risk prior to starting the event or evolution The ability to assign numerical values or color codes to hazards using the GAR Model is not the most important part of risk assessment What is critical to this step is team discussions leading to an understanding of the risks and how they will be managed Table 1 1 NETN Phenology Monitoring Protocol assigned risk codes of 0 For No Risk through 10 For Maximum Risk to each of the eight Green Amber Red Risk Assessment elements Element Rating Supervision 4 Planning Communication C
346. vises the default score cutoff of 0 1 with a unique value for ach templat CORtemplates lt templateCutoff CORtemplates score cutoff c BTINW_rect_C 0 4 BTNW_rect_MandHnotes_C 0 45 BTNW_rect_d80_C 0 41 BTNW_rect_d50_C 0 38 BTNW_rect_d20_C 0 42 BTNW_auto_d100_C 0 41 BTNW_auto_d80_C 0 4 BTNW_auto_d20_C 0 35 BTNW_line_d100_C 0 29 BTNWlineO 5_C 0 42 BINW_click_allNotes_C 0 41 This call assigns a new default value for all templates CORtemplates lt templateCutoff CORtemplates score cutoff c default 0 40 Rename templates too CORtemplates lt templateNames CORtemplates c vector of new names The print method for this class returns a summary of all templates in the list when called gt CORtemplates Object of class corTemplateList containing 11 templates original recording sample rate BINW_auto_d100_C Dropbox LabDemo Templates BTNW wav 24000 BINW_auto_d20_C Dropbox LabDemo Templates BTNW wav 24000 BINW_auto_d80_C Dropbox LabDemo Templates BTNW wav 24000 BTNW_click_allNotes_C Dropbox LabDemo Templates BTNW wav 24000 BTNWlineO Dropbox LabDemo Templates BTINW wav 24000 BTNW_line_d100_cC Dropbox LabDemo Templates BTINW wav 24000 BINW_rect_C Dropbox LabDemo Templates BTNW wav 24000 BINW_rect_d20_C Dropbox LabDemo Templates BTINW wav 24000 BINW_rect_d50_C Dropbox LabDemo Templates BTNW wav 2400
347. x S1 B Job Safety Analysis continued Potential Hazards Recommended Action or Procedure Bee wasp or Multiple stings from disturbing or Be alert to hives in brush ground holes or yellow jacket stepping into nest areas hollow logs Watch for insects traveling in and stings out of one location If you are allergic to bee stings tell your partner if working in a pair Make sure you carry emergency medication with you at all times and that your partner if applicable knows where you keep it Wear long sleeve shirts and trousers tuck in shirt Bright colors and metal objects may attract bees or wasps If you are stung a cold compress may bring relief If stinger is left behind scrape it off of skin Do not use tweezers as this squeezes the venom sack worsening the injury If the victim develops hives asthmatic breathing tissue swelling or a drop in blood pressure seek medical help immediately Bites from Itchy reactions to multiple bites Wear long sleeves and pants mosquitoes Avoid sitting on the ground or on logs especially black flies and in dry sunny grassy areas other insects Use insect repellants Do not apply Permethrin Permanone or greater than 30 DEET directly to skin only to clothing Carry after bite medication to reduce skin irritation Contracting diseases transmitted Use tick avoidance precautions including pre from ticks treating clothing with permethrin tucking pants into socks and shirt into pa
348. x x Falling leaves x x x x Flowers or flower x x X x buds Open flowers x x x x Pollen release x x Fruits x x x X Ripe fruits Recent fruit or seed x x x x drop Table S12 A 2 Monitored phenophases for evergreen conifers USA NPN Phenophase Balsam fir Breaking needle buds Young needles Pollen cones Open pollen cones Pollen release Unripe seed cones Ripe seed cones x XxX XxX X X X X Recent cone or seed drop 249 SOP 12 Data Analysis and Reporting Appendix 12 A Selected Phenophases for NETN Species continued Table 12 A 3 Monitored phenophases for wildflowers and forbs White Rough Provorhase O24 mustard E Std Sais por margokd DOER poe Initial growth x X xX x xX x x x xX Leaves xX xX xX x X x x x xX Flowers or x xX xX x x x xX x xX flower buds Open flowers x X xX x x x x x x Pollen release Fruits x x xX x X x xX x Ripe fruits x x x x x x x x x Recent fruit or x x x x x x x x x seed drop Table S12 A 4 Monitored phenophases for seaweed Rockweed USA NPN Phenophase Ascophyllum nodosum New side branches x Receptacles x Flat receptacles x Smooth inflated receptacles x Dotted inflated receptacles x Torn receptacles x Table S12 A 5 Monitored phenophases for amphibians USA NPN Spotted Phenophase Senda Spring peeper Wood frog Adults on land x x x Adults in water x x Xx Adults feeding x x x Vocalizing xX x Mating xX x Fresh eggs x x Dead adul
349. xpensive time lapse cameras can provide a more complete observational record of individual plants at a subset of sites Crimmins and Crimmins 2008 and also allows for automated detection of certain phenophases at the individual and stand scales Richardson et al 2009 When cameras are focused on individuals that are also the focus of volunteer observations the photographs can serve as a quality control check on the volunteers Automated camera monitoring requires equipment cameras batteries and memory cards as well as staff or volunteer time to test deploy check download data and manage data Individual parks must determine whether they want to implement camera monitoring based on their available funding expertise and interests Automated audio monitoring with autonomous recording units ARUs is well suited to capturing the breeding phenology of vocal anurans frogs and toads songbirds and some insects as well as trends in the general soundscape Kasten et al 2012 ARUs collect data at a subset of phenology sites providing a detailed acoustic record for the site These recordings can be reviewed by experts to identify species but this approach is time consuming NETN uses automated methods to identify indicator species whose vocalizations are well suited to automatic detection The recordings are retained in case detectors for additional species are added in the future and for potential evaluation by experts for additional spe
350. y Server Local file Directio Remote file Size Priority Status Queued files Failed transfers Successful transfers 12 wn Queue empty To sign off click on the button highlighted in red above 241 SOP 12 Data Analysis and Reporting Northeast Temperate Network Version 1 00 Overview This SOP describes analysis and reporting of long term phenology data Phenology data is collected onsite in participating NETN parks by staff and volunteer observers as well as by automatic cameras and automatic recording units ARUs Associated environmental data are compiled from nearby weather stations Statistical analysis will be performed in the R software package or an alternative package selected by NETN Objectives Our data analysis objectives are e Detect change in timing and abundance of monitored phenophases of key species at index sites in designated core and optional park habitats e Explore correlations between phenological data and climate variables including mean temperature and degree days in order to develop hypotheses about impacts of climate change on phenology Observer Data Annually the NETN data manager obtains NPS Northeast Temperate Network data in the National Phenology Database using the online data download tool at www usanpn org results data In the data download menu go to Partner Organization select Primary Network to be National Park Service in the first box Northeast Temperate Network
351. y used for monitoring birds or other taxa although it will consume power at the same rate as the SM1 depicted in the earlier graphs Figure S6 7 can help when choosing how to power and how much storage to provide for bat and mixed bat bird recording configurations The exclusive bat recording schedule assumes no triggering and12 hour bat recording and the mixed recording schedule assumes no triggering and 12 hour days nights Note that analysis of ultrasonic recordings can be done according to the procedures in SOP 7 Acoustic Template Creation and SOP 8 Automated Sound Detection and Classification but that there is good off the shelf software available that can classify ultrasonic bat recordings NETN has a license for SonoBat and Wildlife Acoustics has recently released bat detection software Kaleidoscope Pro Standard deployment of SM units for phenology monitoring of birds and amphibians in NETN parks uses a sampling rate of 24 kHz The current recommended sampling schedule is to record 5 minutes at the top of each hour as per the Terrestrial Wetland Global Change Research Network TWGCRN protocol Detection probabilities are species specific but a lower estimate across numerous bird species during a five minute point count is 0 55 Using this protocol and assuming a detection probability of 0 55 for all species there is a greater than 95 probability that a species will be recorded vocalizing in at least one of four consecutive recording

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