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CPW Photo Warehouse User Guide

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1. Initial Setup To set up a blank copy of the database for use with a new project there are 4 steps to get everything ready to go The forms for completing these steps can all be accessed from the Switchboard form which is displayed when you first open the database Before you start this process make sure you have a list of camera locations including UTM coordinates if available ready It can also help to compile a list of the species you expect to appear in your photos including Latin names and a list of any additional details you might want to add when assigning the species to photos e g sex age collared or not It s also a good idea to create a blank copy of the database before you set it up in case something goes wrong and you want to start the process over from scratch First you must add at least one study area to the StudyAreas table Figure 5 Switchboard gt Add or Edit Study Areas If your project doesn t include multiple distinct study areas a single all encompassing study area name will do but you cannot enter information for camera deployments until this step is complete Study areas should represent distinct groups of camera locations geographic regions control vs treatment habitat strata etc that you may want to summarize separately or compare later on gt Telluride f Highway 145 corridor between Telluride and Lizard Head P Molas Pass MP Highway 550 corridor near Molas Pass B Ji
2. CPw Photo Warehouse User Guide gm COLORADO Page 1 S Parks and Wildlife All content 2015 Colorado Parks and Wildlife unless otherwise noted The Cpw Photo Warehouse was designed by Eric Newkirk for Jacob S Ivan at Colorado Parks and Wildlife Mammals Research Section Fort Collins CO Suggested citation Newkirk E S 2014 CPw Photo Warehouse Colorado Parks and Wildlife Fort Collins Colorado USA http cpw state co us learn Pages ResearchMammalsSoftware aspx Acknowledgements Special thanks to Kevin Crooks and Jesse Lewis at Colorado State University CSU for help with funding and guidance with earlier versions of the generic photo database and to Mary Schuette for developing critical aspects of the initial Colorado Parks and Wildlife CPW Lynx Occupancy database Thanks also to Kevin Blecha CPW CSU Stewart Breck USDA NWRC Reesa Conrey CPW Joe Halseth CPW Rebecca Much CSU USDA NWRC Lani Stinson CPW CSU Matthew Strauser CPW and Colin Wait CSU for testing feedback and patience License This program is free software you can redistribute it and or modify it under the terms of the included license To view the license agreement click the Credits link on the startup form then click License Agreement This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the
3. Edit the Species List on the Switchboard In the form that appears click the delete button to the right of the record you want to discard Bear in our example A prompt will appear asking if you re sure and the database will then check to see if any photos have been assigned that species in our example we know this is true since User B applied the Bear ID to a few photos Because there are IDs for the species we re deleting a second prompt will appear asking whether those IDs should be switched to something else before Bear is deleted from the list Clicking Yes brings up a simple pop up form Figure 15 On the left in the Species to Delete field you see the common name Bear for the record you chose to delete on the right is a drop down with the other species in your list Selecting Black Bear on the right and clicking the Merge button will switch all Bear IDs to Black Bear and delete Bear from the Species table then reevaluate the detections table to see if records flagged pending can now be verified ee Species to delete Species to keep Person BE Human rge Photo ID Species Figure 15 Merging species entries If you choose not to switch the IDs for a particular species when you delete it the IDs will be discarded when the species is removed from the table If you click yes to switch IDs to a different species but then change your mind and cancel the merge
4. you can delete both the records and the images COLORADO Page 27 Parks and Wildlife Department of Natural Resources A Updating the Path for Photos If you move any of the folders containing photos you ve imported the database won t be able to display them To fix this use the Update Folder Location command from the startup form This opens a form in which you can select a folder location from the Photos table then browse to the new location for those photos When you click the Update button every photo that referenced the location you selected will be updated to the new location This means you can t update a location for a single photo at a time through this form If you move a single photo from one folder to another while leaving others untouched you ll have to update the location manually in the Photos table so don t do it If you use an external hard drive to store your photos the drive letter can change when you switch computers or plug in other drives If that happens click the Update drive letter link on the Update Folder form select the old drive letter and enter the new letter for the drive If you ve moved or renamed a few photos but not an entire folder you can restore the link to those few photos by double clicking the empty image frame on the PhotolD or PhotoViewer form while viewing the appropriate record then browsing to the correct photo Identifying Individuals If your photos
5. Canadalynx 0 022 Quiet Period minutes 60 lCanadalynx 0 024 lCanadaiynx 0 044 Use Study Areas 1 Canadatynx 0 055 Use Custom Zones 1 Canadatynx 0 117 1 Canadatynx 0 149 1 Canadatynx 0152 1 Canadalynx 0 167 1 Canada lynx 0 169 mx Zone Options Time Feld Calculation Options Decimal C Radians Location Filters Study Area North of South of East of West of Date Filters ws 1 Canadatynx 0 339 lCanadalynx 0 440 1 Canadalynx 0 562 lCanadalynx 0 588 Relative Date Filters 1 Canadalynx 0 608 Starting Days after set date 1 Canadalynx 0615 Ending Weeks lt aferstart 1 Canadalynx 0 674 Absolute Date Filters Images between And Additional Fields Image Date Location Neme UTM Fields pae T Gee e Gabe Clove nx 2Canadalynk 0 148 2Canadalynx 0151 i ms Figure 24 Activity Pattern Query Builder The Require 2 Observers box and location filter fields work exactly like they do on the occupancy form The species selection box works the same as well but you also have the option to include multiple species To do so click the Select Multiple Species button and check the box next to each species you want to include Below the species selection section you can specify a quiet period in minutes The quiet period is the minimum interval between subsequent detections at the same location The preferred quiet period in the literature seems to be 30 minutes but
6. JI Record M 1of2 M W Wk NoFilter Search Figure 5 Adding study areas COLORADO Page 10 Parks and Wildlife Department of Natural Resources AG The next step is to add camera location information Figure 6 Switchboard gt Add or Edit Locations You can enter information for all of the camera locations at once when first setting up the database or you can add some now and continue the process later but you can t import photos until you have records in the locations table Enter each camera location on a separate line Every location must be associated with a study area and must be given a name but the other fields are optional Comeratocations Camera Locations Telluride Telluride Telluride Telluride Telluride Telluride Telluride Telluride Telluride Telluride Telluride Telluride Telluride Telluride Figure 6 Adding camera locations Another option is to paste location records from a spreadsheet but be careful with this process since it can be easy to make a mess of things With the camera locations form open open the spreadsheet that contains your location data For the copy to be successful the fields in your spreadsheet must be in exactly the same order that they appear in the form and you can t skip any columns With your spreadsheet rearranged to match the form select all the rows you want to paste If your spreadsheet has a header ro
7. The PhotoID form displays the photos you ve imported one at a time along with a subform for identifying the species present in each photo Double clicking on the image will open it in your default photo viewing application where you will be able to zoom pan etc There are some simple filter options in the form s header section that allow you to restrict which images the form displays the season filter uses the year from the set date not the date the photo was taken x iex ux Figure 13 PhotolD form COLORADO Page 16 Parks and Wildlife Department of Natural Resources To assign species to a photo select the appropriate species in the drop down box at the bottom left You can assign multiple species to the same photo by adding additional rows in the subform If you want you can also assign a specific detail related to the species you ve selected There is also a field for the number of individuals of this species present in the image default is 1 and a field for comments Also note the Highlight checkbox on the right side tick this box to flag particularly interesting photos Highlights can be easily retrieved later on for use in reports or presentations for example Once you ve created a row in the subform for each species present in an image use the Next button to move on Don t just skip photos with nothing in them specify None as the ID Otherwise you won t be able to
8. active such as noon for mountain lions You can limit the data included in your query by using the filter fields You can select a particular study area or year or you can enter UTMs to limit the data geographically If you choose to filter by year note that the year of the date the camera was set will be used If you choose to filter using UTMs your locations must all be converted to the same UTM zone for the filters to work properly If you experience performance issues while using the occupancy form try un checking the Auto update results box near the top When the box is checked and you change a parameter in one of the fields on the left the form waits about 2 seconds for further changes then updates the results This can be clunky and the form may work more smoothly if you uncheck the box while making changes then check it only when you want the results to update When you re happy with the query you ve created you can save the results by clicking the Export button Choose a format spreadsheet or MARK input file and specify a name and location for the new file Check the view output box if you want to open the file in Windows once it s created If you choose to export to a spreadsheet your settings and filters will be detailed on a separate sheet within the workbook If you export to a text input file the settings will be listed in the header of the text file At any time while using the occupancy form you can close it and vi
9. and VBA go for it If not it s better to create your own queries forms etc from scratch so that the original objects remain intact If you want to make a scrap copy of a form or report you must copy any subforms or subreports as well and update the form design to make sure you aren t affecting the original il f Camera Data Tables Other Tables Queries o E Oo i Figure 4 Custom navigation pane view Help Messages Help text is available to guide you through most of the forms you ll be using in the database To see the help text for a particular form click the blue question mark button in the top right of the form itself not the one at the top right of the Access window You can also view all of the help messages for the database by clicking the Help link on the Switchboard form then clicking View All Help Entries COLORADO Page 8 Parks and Wildlife Department of Natural Resources A Maintenance and Troubleshooting The most important thing to remember when working with this database is to back it up There is a backup option listed in the Office Button menu available if you close the startup form or you can simply make a copy of the accdb file in Windows Back up the database as often as you can remember to do it Another important step that will keep the database running smoothly is to compact and repair it Close the Switchboard form click the Office Button select m
10. as the output format you can choose between two types of detectors proximity and count Count detectors allow for multiple detections of the same individual at the same location within an occasion proximity detectors do not See the documentation for the secr package for more details Make sure to specify the correct detector type when importing your data You may get an error in R if you have detections for occasions when the effort is 0 This can happen when the boundary between occasions is almost but not exactly the ActiveStart or ActiveEnd for a particular location so that the effort is tiny enough to round to 0 You can either delete the detections for that occasion at that location or you can set the effort to 0 01 instead of 0 Another error will appear if you have occasions where the effort is O for all locations To fix it you can change the options on the form to ensure that you have at least some camera activity in each occasion or you can delete the empty occasions from the detector files before you import your data If you change the output format to MARK your results will be pivoted to provide one row per individual and capture histories will follow traditional 0 1 formatting Binary group variables after the capture history identify the session associated with each capture history Additionally effort number of cameras operating by group and occasion is provided in the header of the input file so that you can manually
11. at the time is included with each detection record added to the table and the record is flagged as pending When you close the PhotolD form or import detections from a Photo ID module the records are compared and those that match are flagged as verified meaning the Species Detail and Individuals fields all match Say you have 100 photos in your database and you ID them all logged in as Observer A You now have 100 records in your detections table or more if some photos have more than one species linked to Observer A Your coworker Observer B then works through all the photos independently assigning IDs What you end up with in the Detections table is a mix of records where Observers A and B agree and those where they don t In the first case the records will be marked verified and no further action is needed In the second case both records remain pending in the database and need to be reconciled by a referee You can have more than 2 observers review your photos if you like Imagine a second coworker Observer C looks through the photos from the example above There are now several possibilities A B and C can all agree none can agree or any combination of 2 observers can agree In the cases where all observers agree your Detections table will simply contain three verified detections with the same information In any case where the observers disagree however there will be pending detection records in the table and the IDs ne
12. clicking the Add New Location button Note that subfolders are not necessarily included so a database saved in a folder within My Documents may not work even if My Documents is a trusted location If you want subfolders of a particular location to be trusted make sure to check the box for that option Now you can save the database to your chosen folder if you haven t already and when double clicked it should open as in Figure 1 COLORADO Page 5 Parks and Wildlife Department of Natural Resources Understanding the Database It s important to know a little about the purpose and limitations of the database before you get started You don t have to be an expert in Access to use the database in fact you don t need any experience with Access at all Think of the database as a catalog of all your photos It doesn t actually contain any of the images themselves Instead it stores the metadata associated with them such as the date taken and the species present Using forms and VBA code it s possible to automate much of the cataloging process and to make the processes that require user input such as identifying the species in the photos work much more smoothly In addition the forms link and display the photos represented in the data eliminating the need to move back and forth between photo viewing and data entry programs To use an analogy think of the database like a card catalog in a library You can t
13. copies of all the photos in exchange for their permission You could filter the PhotoViewer form to that particular location then use the Copy Photos button to create a folder with all the applicable photos In another case you might be collaborating with someone who is interested in all of your photos of a particular species You can filter PhotoViewer to display only photos of that species then use the Copy Photos button to create a folder of images to send off For an explanation of the include runtime database option see Distributing photos for others to ID above Deleting Photos Click the Delete Photos button on the PhotoViewer form to delete all of the photos that match your current filters similar to the process for copying photos There are 3 options available when you want to delete photos You can delete just the jpg files but maintain the records in the database delete the records but maintain the files or delete both Here area few examples if you have a ton of photos with nothing in them and you re tired of looking at them you may want to delete the records for those files but maintain the jpgs for the sake of keeping a complete archive On the other hand you may want to clear some space on your hard drive by deleting the jpg files with nothing in them but maintain the records in the database so you know those photos existed If you made a mistake importing some files and want to start from scratch
14. include the effort through the design matrix in MARK if you wish Keep in mind regardless of which mark recapture analysis you choose that some detections of individuals may be dependent on others which can cause unwanted results For example if you repeatedly get pictures of a female mountain lion with her offspring those individuals will appear as separate lines in the input file but their detections were not truly independent In this case you should delete the rows associated with the kitten to avoid misrepresenting the individuals as independent and overstating the precision of your estimates COLORADO Page 40 Parks and Wildlife Department of Natural Resources A Database Objects Queries There are a few utility and summary queries saved in the database in the Queries category of the navigation pane Summary queries group your camera data by year study area or deployment and provide some basic statistics about how long the cameras were deployed and how many photos were collected Missing Photos and Missing Photo Folders find records for which the jpeg file cannot be found Occupancy Query is the query that s overwritten each time you create a query through the OccupancyQueryBuilder form and the same goes for SECR Query and SECR Detector Query Activity Pattern Query is similar but it can only be opened while the ActivityQueryBuilder form is open Photo Viewer Query is the query that s overwritten each time you press
15. included license for more details The license agreement is also available at http cpw state co us learn Pages ResearchMammalsSoftware aspx Contact cpwphotodb gmail com COLORADO Page 2 Parks and Wildlife Department of Natural Resources A Table of Contents General INFOMMAVOM s ssscscisreasearee ttn rte RR oer ER SER ERU mentees E E PATI PAR DE EDO DUE PED DM FEE 4 dieWantiniie me ausara sE EE EEEE EAEE SEENE 4 Enabling VBA COJE icc2ssccnen ih neeswedswanee URN GERE T EG A RS Ga EEE E dH INFERNA 4 Understanding the Database sisssesen ne rtr RR Rex RE ER RH R E TREREX RPXT Rau SP ESQ ETE FEFFEEPRP FEN EP DF SU EEEME 6 MME SWIECHDOALG FORM uo occ Re THREE RO SIRE ERREUR ES AUR e MI GREEN UR RUE UP EEEE 7 THE NAVIGATION Pallet n RE E EX REA nS RE UE RE MT M MU SURE LIEST ENMPIUN DDR E HPEN EEE ER 8 Help Messages iucscessteie me e RE Re RI E ERR E Nee RR A EIS PIE PIA e A DIETE PP PETS Pe FPE EE d E ENE EEE EERE 8 Maintenance and Troubleshooting 0 eR rure E E E m RT I Ie E e E EIE Reg E M IR P EID EI US E PD EUER PES eEAE 9 Blpcuiuree 9 Using Rd MULA 10 Initial Setup e 10 Adding Visits sois e Roe I IR Ee AU D E ER E R E RID M pA D EHPuEU E NN DI P MU MU PD MICI UI EN Uer ME E NUES 12 Importing PhOtOS s i esoeos ores o ure E D Re E e RI RR N Re E T E M iR E DIN EHE
16. selecting the individual s name in the drop down above the buttons for editing detection events The photos will appear in a pop up form which you can leave open while you work You can select different photos through the form and they don t necessarily have to be photos from your camera data but keep in mind that if you move the database without moving the reference photos the links will break just like the ones in your camera data If you can t determine which individual is present in a given event you can select Unknown from the drop down in the subform to indicate that the event has been reviewed The individuals list accessible via the link in the lower right corner is very straightforward and works similarly to the species list described above COLORADO Page 30 Parks and Wildlife Department of Natural Resources A Analyzing Data Occupancy Analysis The OccupancyQueryBuilder form Figure 21 Switchboard gt Build an Occupancy Query allows you to export data from your database for use in single species single season analysis in MARK or RMARK It contains a results preview pane on the right and a set of filters and options on the left No results will display until you ve selected a species at the top of the form Select the species Canada Lynx Results Preview Dad P testion Occasioni Occasion2 Occasion Occasion Occasions Occasion Occasion StudyArea SurveyYear CameraUT
17. separate input files for detections and detectors if you export to a spreadsheet these will be included as separate sheets within the same excel file but if you export directly to txt there will be two separate files created Trap effort based on the active dates in the visits table is included in the detector file for each location each number represents the proportion of that occasion for which the camera was operating from 0 to 1 If you don t want to include the effort covariates in your analysis you can add 7 before them on each line If you do choose to include them make sure you set binary usage FALSE when you import the files into R like this library secr setwd C Users DoeJ Documents myData lt read capthist secrdata txt secrdataTrapsTelluridel txt detector proximity binary usage FALSE plot myData results lt secr fit myData results COLORADO Page 39 Parks and Wildlife Department of Natural Resources If your data includes multiple sessions there will be a separate detector file for each session Be careful when importing these files using the read capthist function you must specify the files in the correct order for the data to import correctly the order is based on alphanumeric sorting of sessions Keep in mind that if you change the sessions as described in the paragraph above you will need to rearrange the detector files to match your new sessions When secr is selected
18. the individual level they will remain empty The Switchboardltems table contains the data required for the startup form to function and Help stores the text displayed in custom help messages Observers names and contact information are stored in the Observers and ObsPhone tables COLORADO Page 42 Parks and Wildlife Department of Natural Resources A There are several lookup tables that contain text values for the various ID s stored in the database Storing an integer ID in the data tables and the corresponding text value in a lookup table saves space and improves performance DetectionDetails Species and StudyAreas all function as lookups in this database Lookup tables can also contain other information about the items in the list that may come in handy at some point such as the LatinName field in the Species table The following diagram Figure 266 provides a graphical representation of the relationships between the major tables in the database To simplify the diagram lookup tables have been omitted All lookup tables utilize one to many relationships with referential integrity enforced StudyAreas 9 StudyArealD StudyAreaName StudyAreaAbbr StudyAreaDescripti CameraLocations Y LocationiD StudyArealD LocationName Visits visitiD LocationID VisitTypeID VisitDate Comments ActiveStart ActiveEnd Photos ImagelD ImageNum I
19. you can enter whatever you like A quiet period of 0 means that all photos will be included in the results If you set your quiet period and get results that don t seem to make sense remember that the quiet period only applies to photos from a single location for a single species For example if you set your quiet period to 30 minutes and your first detection is at midnight no results from COLORADO Page 36 Parks and Wildlife Department of Natural Resources that location will be included until at least 12 30 AM However you could still have an included detection at 12 01 AM if it s from a different location There are two options for grouping your locations into zones You can use study areas as Zones or you can assign custom zones yourself If you decide to assign your own be aware that any location which isn t assigned a zone will be omitted from the results which can be useful if you want to exclude a few locations Press the button labeled Edit Custom Zones to change which locations are assigned to each zone Once you have your zones figured out hours 60 minutes 1440 decimal days 2m The first step in analyzing your results in R is to convert to radians so if you plan on using OVERLAP you might as well export your data in radians and save a step you can choose whether you want your results in decimal days or radians In addition to the location filters you have the option to filter your results by date based on a hard
20. 2 14 2013 Molas Pass Cama check 1 14 2014 12 14 13 16 12 30 1 14 14 16 53 00 Molas Pass Cam4 Pur z amp 2014 1 17 145 20 46 2 8 14 15 50 58 MolasPass Cams set 12 17 2013 MolasPass Cams check 1 14 2014 12 17 13 16 05 42 1 14 14 15 31 26 Bo Figure 23 Editing active dates from Occupancy form COLORADO Page 35 Parks and Wildlife Department of Natural Resources Activity Pattern Analysis Creating an activity pattern query is very similar to the process described above but there are a few key differences Activity pattern results are formatted for the R package OVERLAP Click Build an Activity Pattern Query on the Switchboard to open the ActivityQueryBuilder form Figure 24 Activity pattern results consist of a zone column a species column and a time column Each row represents a single photo in which a particular species was detected The ActivityQueryBuilder form looks very similar to the occupancy form but behind the scenes it works quite differently It requires a temporary copy of your database to function so if you notice an extra copy of your accdb file in the same folder with AP added to the name don t delete it It will be deleted when the activity form is closed 3 AdivityQueryBuilder Activity Query Builder Select tha spacio Canada Lynx E Ato UpdseResis W Results Preview Ce tei D E fee loses Tine z E 1
21. Builder Occupancy input files follow typical capture history format but each row represents a camera deployment rather than a particular individual If the species of interest was detected during a particular occasion the column corresponding to that occasion contains a 1 If the species of interest was not detected during a particular occasion the corresponding column contains a zero If the camera was not functional for any part of an occasion it is represented with a Uncheck the box labeled Require 2 Observers if you want to count detections that have only been entered by one observer This makes sense if you don t have two independent observers ID ing all your photos Note that if the box is checked and some of your photos have only been reviewed once or not at all those rows will have 0 s in the occasion columns not For this reason you should only generate occupancy queries with the 2 observer box checked for deployments that have been reviewed by 2 observers and for which all mismatched IDs have been reviewed and corrected If you have some data that s ready to go COLORADO Page 31 Parks and Wildlife Department of Natural Resources and some that isn t you can use the filters to weed out data that hasn t been fully reviewed yet or you can uncheck the box to accept single observer IDs The fields under the Start Date Options heading control when the first occasion begins for each deploym
22. Cancel so don t just hit the Enter key Saving the module file in a trusted location will avoid the security warnings altogether It may take a while for the import operation to run depending on the number of photos in the module but when it finishes you will be notified of the number of detections that were added and how they were flagged In some situations you may get more detections than you expect from a module This indicates that some of the photos in the module have more than one associated detection either because they contain more than one species or more than one observer used the same module database to ID photos COLORADO Page 22 Parks and Wildlife Department of Natural Resources A9 Managing the Species and Detail Lists When multiple users ID photos using modules the species and detail lists inevitably get a little sloppy Imagine Observer A and Observer B both complete a module that includes a few photos of a black bear but that hasn t been added to the species list yet Observer A reaches those photos and adds a new record to the Species table with a common name of Black Bear but when Observer B adds the new record they simply put Bear in the common name field When the IDs from Observer B are imported Bear will be added separately to your species list because it doesn t match the existing record and the IDs for those photos will be considered unmatched To fix this click the button labeled
23. EE 28 Identifyrmg JIndividuals tes cne sean E a E ORO PD I NEP ETE 28 Analyzing Data cerai reses E NON WR EE E E EE EEEE 31 OCCUPANCY ANALYSIS EET EE 31 Adjusting Active Dates for Occupancy AnalySisS ceecceeeee eee ee eee e eee eee ene e he e ehe nhe enne enne 33 Activity Pattern Analysis sisse rh RR REX REX RGR X GN RS X RGN RR G3 R SEEE EEE EEEE ES ESEE ENERE UH PU OUR 36 Mark Recapture Analysis 5 3 2 0 actin GG Ra AG NR SQ S sa aan IT KR SC ORG OUR A OU NU RUKDPENN LONE RUIN MUDETNSIN ENS 39 Database Objects icis c ince incsscicen scan RO XA GG KXGR PRG SRG SEX KXGO RR GR KR GIO soandinay seaman de KEPE FEYCMEPA PEE PEPNMPP EPUM EVE 39 Quieres oceeveve ve eve va e ove va e o ve va Yn eva VA YA PA NA VA VA NA NA EA NA VA EA NA VAN EA NA VA ANA Va VA ed veu a vedo vea EEEE ku 41 pp Lc M 41 Itl e 42 COLORADO Page 3 Parks and Wildlife Department of Natural Resources General Information Field Considerations There are a few things you can do when collecting camera trapping data that will make working with the database much easier First make sure you have a system in place to keep track of where and when each camera was deployed If your cameras have a programmable user label that will appear in each photo use that as
24. M CameraUTM StartDateTime Start Date Options T Uizardi 2014 244444 4184444 1 8 2014 Relative First occasion starts 1 days after camera set date v 2014 244444 4183424 1 8 2014 C Absolute T Ophiri 2013 244444 4184444 12 21 2013 Start Time noe bles to uni time Bon first poto pA T Ophir2 View Edit Active Dates T Ophir2 Interval Options T Homel Number of eccasions 7 T Home2 T Home3 T Homes T Homes Filters T Uzards 2014 244444 4184444 2 17 2014 2013 244444 184444 12 21 2013 2014 224444 4184444 2 19 2014 2014 244444 4184444 2 12 2014 2014 244444 4184444 2 12 2014 2014 244444 am 2 12 2014 3014 244444 aisa 2 18 2014 4184444 2 15 2014 2014 244444 4184444 2 15 2014 2014 244444 4184444 2 16 2014 2014 244444 4184444 2 13 2014 2014 244444 4184444 2 1 2014 2014 244444 amm 1 31 2014 2014 284444 4184444 2 6 2014 2014 209444 4184444 2 6 2014 2014 244444 4184444 2 23 2014 2014 244444 4184444 2 22 2014 2014 244444 4184444 2 23 2014 Study Ares Telluride ES I piv T Duntont T Altat T Alta2 T Alta3 T Alta4 Survey year iei T LizardiB T Ophir J EN T Hopes South of East of West of a e oeocooocoooccocoocccoo coco 0o0o00o0o00o0c0cocoroco o6050 o06o0006000o0c5cr5 o 66 6 6005 0606060 50665 o wee eee 0600 6066025 6 o 0 0090 0000 005600000 eee ooocooooco ocococcseo coven Query iF I tae Im EMNER jeoesue Figure 21 Occupancy Query
25. M TM M DN PNEU IN EMEN M TENE 15 TASTING SPSCIOS cienia E A R EN T EE NEEE EEEE EE ERAN 16 Using Keyboard Shortcuts wee cisetdcasctedevetstetdvavciecdwcdhbecdvevatarawcdhtacdved gee avere e UU EEEE SETE EE EREE 18 Using the Batch ID Feature ie cicctacscctederetitetdvasclecdwcdhbecdvevatatawcbhtadvedede devonsvendeewmecudensoueslewtveuetes 19 Distributing Photos for Others tO IDs ia cs exeo xo tecadcsseeradagemndens deaaematdsangons gegedeangeahooeseegrangnneasan enon 20 Photo ID ODSerVels s execesexoseto et ex Ret aaa od obedsued adedoasgadcatdsasceun ROPIC Oz NN EUMD PU URDRERU OPER 21 lmporting IDs from a PhotolD Module 5 rrr reb nre tr rx es brR Ee rr Era n Ea E p E E E CR E EFE PEE 22 Managing the Species and Detail Lists eere einer Irt he rk rbrh Kr bha I RR RR siden EREPE RU RRMESR RN RUR E REM EP ES 23 senec 24 Using the PhotoViewer TOIT uoce enr rr ttn rto nre hr tEn n o E EHE REN E ER T OR E TUE FUE ER TE EEREEE A ES E EE EN VERS VERE UE 26 Creating a Query With Photo Data ror rere e Imre S p E EIS E D E S DI M Id E S Ru E MEDIE ISIN ME pn M MENFES 27 COPYING PROLOS coiere ee o n d Ee Er IR E d E E mede EqrE d UO E E DIIS tastes NU UM ME LU NU IPIS NUM NUN VEE 27 Deleting Photos errore e tees te novere Eann ste sese ve EE ONT NEEESE OE EEE ede REE ESENE E ESE ERE EEEREN Eua 27 Updating the Path for Photos o rrerr rr tre etr etr ne ir aiet NN R EE NEE E ESERE EEEE EEE ES
26. View Query Results Copy Photos or Delete Photos from the PhotoViewer form Observer Comparison and Photo ID Summary provide the raw data behind the associated reports Reports Several reports are included to help you manage and summarize your data To access them click View Print a Report on the Switchboard form then select a report and press the button to generate it The Camera Data Summary report combines the summary queries mentioned above to provide summary statistics about your camera deployments Statistics are calculated first by year then within each year by study area then finally for each individual deployment Camera Pull Checklist provides a list of all the cameras for which you ve entered a set visit but have not entered a pull visit Access Notes is exactly what it sounds like a list of the access instructions that have been entered for each of your camera locations and the Contact List report retrieves the data from the Observers table The Photo ID Summary report is designed to help you keep track of which photos have been processed and which haven t It s formatted as a list of all your camera deployments with the total photos collected for each how many of those photos have had at least one species assigned how many have verified species IDs and a list of the initials of the observers who have worked on the photos for that deployment When some work has been done on a group of photos the loca
27. VisitTypelD column and the date of the visit is recorded in VisitDate The start and end times used in occupancy queries are recorded in the ActiveStart and ActiveEnd fields Photos is related to Visits on the VisitID field It contains a record for every photo imported into the database The date time folder location and file name are automatically added to the table when the photos are imported There is also a Highlight field used to flag particularly interesting photos It s not a good idea to enter photo records manually always use the Import Photos option from the startup form to add photo records Detections is related to Photos using the ImagelD field and is used to store the species SpeciesID related to the Species table present for each photo Because these are stored in a separate table there can be more than one species recorded for each photo Detections also contains a DetaillD field related to the DetectionDetails table for adding specific details about the species present for example On Leash if the species is dog The field Individuals stores the number of individuals present in the photo for each species and the Comments field can be used to add additional information There are also fields that record the observer s associated with each detection record IndependentDetections IndividualDetections and Individuals contain the data regarding individuals present in your photos If you never identify your photos to
28. a failsafe Second try to avoid viewing your photos on other devices before importing them Some digital cameras or phones can permanently damage the photos or metadata on your memory cards when you use them to view photos Others won t be able to view the photos or navigate folder structures and still others will create hidden thumbnail files that can cause problems later on If you need to view photos in the field a laptop is the safest option Finally it s always a good idea to intentionally trigger the camera when you first set it whenever you check it and when you retrieve it Often in analyzing your data you will need to know exactly when a camera was active and having these photos makes that relatively simple These photos combined with well kept records can also help in solving issues later on e g date on the camera was set incorrectly incorrect user label etc Enabling VBA Code The database won t work correctly if the VBA code contained in the forms is blocked When the database opens the Access window should be a blank blue background with just the switchboard form showing Figure 1 If the ribbon top menu bar and navigation pane left menu bar are visible when the database opens that means VBA is being blocked Figure 2 You should also receive a message noting this just below the ribbon and a form named Startup will display some text addressing the situation Using the database in this state can cause all sort
29. ake a book off the shelf and toss it in the trash but the card in the catalog would remain Conversely you can pull a card from the catalog and leave the book on the shelf In either case your catalog will become out of sync with the objects it s meant to represent This database is no different deleting a record from the database is like pulling a card from the catalog and deleting a jpeg file is like throwing out the book Either way the database will end up out of sync with the photos you ve collected To keep the database synced with your photos be as organized when working with the jpeg files as you possibly can be It s highly recommended that you import all of your photos directly from memory cards store them in a simple logical folder hierarchy and rename them consistently also recommend using the import function in the database to copy and rename images from memory cards as this ensures uniformity in that process There is a form in the database for updating the location of a folder when it has moved but if you store your photos in a maze of subfolders or scattered locations it will be difficult to keep track of what you have and where You can use the database itself to view or work with your photos in subsets based on their metadata so it shouldn t be necessary to store them in subfolders based on species or similar attributes On the other hand a storage scheme that is too simple can also cause problems Windows can
30. anage and click compact and repair This gets rid of bloat in the tables and indices within the database file so it will usually shrink the file size quite a bit as well as boost performance If you don t compact and repair once in a while the database will get very sluggish over time If you re experiencing problems or error messages when using the database there are a few things you can try First double check that you re running the database from a trusted location If not check out the General Information section above The next step is to compact and repair the database following the instructions in the last paragraph If you re having trouble even opening the file try holding down the shift key while opening it then try to compact and repair You may experience error messages or the database may fail to open if you move it to a computer running a different version of Access If that s the case open the database you may need to hold down the shift key then open the code window by clicking Database Tools Visual Basic Within the code window click Tools then References Look for any reference marked Missing and find the closest replacement usually the name will be the same but the number at the end will be slightly different in the list Check the box for the correct reference and uncheck the box for the missing one Once all missing references have been resolved click the save button then Com
31. ard Shortcuts Using the mouse to identify species can be unwieldy and time consuming so there are keyboard shortcuts available when using the PhotolD form These are based on the ShortcutKey field in the Species and DetectionDetails tables To see a list of keyboard shortcuts available click the link below the Next and Previous buttons These shortcuts will only work when the focus is on the main form not within the subform where species are listed This can be tricky to figure out but if the keyboard shortcuts aren t working try clicking the Next button then click Previous to return to the record you were on this ensures that the main form has the focus In addition to the shortcuts specific to a species or detail you can use the Z key to repeat all of the data from the last photo and you can use the digit keys 1 through 9 to set the number in the Individuals field You can also use the up down left and right arrows to move between records Getting this system down can take some practice but once you learn how to use it you will be able to work through hundreds of photos in no time There are a couple of situations to note when using the shortcut keys first detail shortcuts will only work if the appropriate species has already been assigned Otherwise the species shortcut will take precedence if it exists For example imagine D is the shortcut for dog L is the shortcut for lynx both in the Sp
32. by pressing Cancel on the merge form you will have another chance to cancel the species deletion Managing the details list works exactly the same way click Edit Species Details on the Switchboard to get started COLORADO Page 23 Parks and Wildlife Department of Natural Resources A Reconciling IDs As mentioned above detections that don t match must be reconciled by a referee to do so click Compare IDs from the Switchboard form This will open the PhotolD form in a special mode Figure 16 and only those photos with pending IDs and two or more observers will be loaded into the form Verified detections appear in black and pending detections appear in red For each photo simply click the X next to all incorrect IDs to mark them deleted in the table The information will be kept but the ID will disappear from the form and any remaining detections will be changed to verified in the detections table and changed from red to black in the form Figure 17 The same location and season filters are available when comparing IDs that are available when using the PhotolD form in its normal mode but for obvious reasons the Only Images That Need ID checkbox is disabled Figure 16 Comparing IDs COLORADO Page 24 Parks and Wildlife Department of Natural Resources Figure 17 Reconciled ID If several observers have reviewed a photo and some but not all of the IDs a
33. cutoff absolute or date limits relative to the date each camera was set All of the date filters are independent so you can specify an absolute start date with no end date or filter by both absolute and relative dates If you specify an absolute end date one day is added so that photos are excluded starting at midnight the following day meaning the end date is inclusive If you need to specify a date and time for the absolute end date field you should subtract one day to achieve the correct cutoff You can also include additional fields if you like by checking any or all of the boxes in the Additional Fields section Exporting an activity query is similar to the process for occupancy queries but the input file option will create a comma separated values file csv with the settings in the header To import the data from this file into R use the read csv command and make sure to specify that the pound sign should be treated as a comment character otherwise the settings will cause an error Your R code should look something like this libraryCoverlap myData lt read csv C Users DoeJ MyQueryResults csv comment char summary myData SpA lt subset myData Species Red Squirrel SpB subset myData Species Snowshoe Hare spc subset myData Species American Marten overlapPlot spA Time spB Time overlapPlot spA Time spC Time overlapPlot spB Time spc Time If you export to a spreadsheet your se
34. dding Visits Once your camera locations have been entered the next step in getting your photos into the database is adding visits You can do this ahead of time or when you re ready to load the photos Visits fall into 3 categories Set Check and Pull A set visit identifies the date when a given camera began sampling i e no photos were being taken before that date A check means the camera was sampling both before and after the visit took place and a pull means A9 COLORADO Page 12 Parks and Wildlife Department of Natural Resources the camera was not operating after that date The period of time from a set visit at a particular location to the following pull visit may be referred to as a deployment Start by clicking Add or Edit Visits on the Switchboard to open the Visits form Figure 9 Select a location in the drop down box at the top of the form select Set for the visit type and fill in the date when the camera was set at that location You can also add comments specific to the visit or access notes for that location also available in the CameraLocations form Click the button to move to the next visit and enter the data for when the camera was checked or pulled You don t have to enter visits in any particular order they will be sorted chronologically next time you use the form so whenever you want to add a new visit just click the Next button until you are past the last visit that s been en
35. differentiate between photos that haven t been looked at yet and those that have been reviewed but don t contain any animals If you try to enter something in the species field that doesn t exist in the Species table Access will prompt you to add a new record to the table If what you entered was just a typo click Cancel to go back and correct it If on the other hand it s a legitimate species that simply hasn t appeared before you can click OK to add the new species to the table A message will appear with simple instructions for adding the species and then the form will pop up Scroll up to make sure that you re not just adding a synonym for a species that s already represented e g cougar versus mountain lion then fill in the Latin name if possible and click Done to add the species to the list You can add a new detail item to the details list the same way Check the Advance Automatically box to have the form move through the records based on the time period you specify like a slideshow To remove a species from a photo click the X button to the right of the comments field If all you care about is the species present in your photos feel free to ignore the Detail and Individuals fields They make ID ing the photos take much longer and aren t necessary for occupancy or activity pattern analysis COLORADO Page 17 Parks and Wildlife Department of Natural Resources AG Using Keybo
36. e is that you can create a standalone database package and send it off to someone else to ID a subset of photos We refer to these packages as modules and they include both a stripped down copy of your database and the photo files to go along with it Start by opening the PhotoViewer form and filtering to the photos you want to distribute more details below Generally it s best to include a maximum of 5 000 to 8 000 photos per module for performance and stability reasons and there s no advantage to creating a large module with lots of photos lumped together versus a few smaller modules Once you have your filters set click the Copy Photos button in PhotoViewer When the CopyPhotos popup appears use the browse dialog to create a new folder for this module Name the folder based on the filters you used in the PhotoViewer form Check the box to include a runtime database with your photos and click Copy When the procedure is done you should have a new file called PhotolD accdr and a folder called Photos within the folder you created The extension accdr means the design of the database can t be edited and the user doesn t need the full version of Access to use it If the person who will be using this module doesn t have MS Access they will need to download the Microsoft Access Runtime installer from the Microsoft website free Your module is now ready for distribution send it to the person who will be lo
37. ecies table and L is also assigned for the detail On Leash associated with the species dog in the DetectionDetails table Pressing D then L will set the species to dog and the detail to On Leash but pressing L first will set the species to lynx The second important point while technically it is possible to add multiple species to a photo using the keyboard shortcuts it s not practical or intuitive By default the shortcuts act on the first record listed in the subform So if the photo in the example above actually had both a dog and a lynx in it pressing L then D wouldn t create the multiple records you need to represent the two different species Instead it would set the species for the first record to lynx then change the species for that record to dog To assign multiple species to a single image as in Figure 13 use keyboard shortcuts to create the first record then use the mouse to add a second record and fill in all the fields To add or customize the shortcuts available for the PhotolD form click the link to display the list and then click the button to edit them This button opens a simple form in which you can edit the ShortcutKey fields in both the Species and DetectionDetails tables Only letters A through Y are allowed for these fields COLORADO Page 18 Parks and Wildlife Department of Natural Resources A Using the Batch ID Feature You can assign the same ID to mul
38. ed to be reviewed Be careful if you have more than three observers review the same photos you can inadvertently end up with strange results Imagine four observers look at a photo of an ungulate and two observers assign deer as the species while the other two enter elk If you add all of these IDs to the database at once all of the detections will be verified because they match another record and your data will look as if both species are present in the photo To prevent this make sure to compare the IDs see below from the first three observers before adding any more COLORADO Page 21 Parks and Wildlife Department of Natural Resources A Importing IDs from a PhotolD Module When someone has worked through all of the photos in a module they can return the PhotolD accdr file via email and delete the jpgs like to rename the file once it s returned with the initials of the person who identified the photos and any other relevant information Wherever you choose to save the module database it s a good idea to make that folder a trusted location To retrieve the ID records from the module open your database not the accdr from the module and click Import Photo ID Module on the Switchboard Browse to the accdr file and click Import If you see security warnings during the import operation it s ABSOLUTELY CRITICAL that you press Open for each warning The default button for these warnings is
39. ent A relative start uses the date of the first photo for a particular deployment and optionally waits a specified number of days afterward before starting the first occasion Leave the days after set date field set to O to start the first occasion when the first photo was taken You can also specify a time to start the first occasion or you can use the time from the first photo taken by that camera For an absolute start date you specify a particular date and time and the first occasion for all deployments begins then Under the Interval Options heading you can specify the number of occasions for each deployment the length of the occasions in days or weeks and the buffer period A buffer period is an amount of time between when one occasion ends and the next begins during which detections will not appear in the results This can be helpful if you have relatively few detections of the species in question and you want to ensure that your occasions are independent For example imagine you have your query set up for 4 one week occasions starting at midnight on June 1 and you re interested in mountain lions You can use a one day buffer period to make sure that a mountain lion that showed up on camera at 11 59 PM on June 6 and stayed until after midnight won t be counted as a 1 for both occasion 1 and occasion 2 Another option for obtaining independent occasions is to specify a start time when you don t expect the species of interest to be
40. ew your results in a new tab by pressing the Open Query button below the settings and filter fields You can also save the query you ve built by pressing the Save button and specifying a name for the new en COLORADO Page 32 Parks and Wildlife Department of Natural Resources query When you want to return to it later on you ll find it in the navigation pane category My Queries Adjusting Active Dates for Occupancy Analysis For the occupancy form to function properly you need an accurate record of when cameras were functioning correctly and when they were not By default the first and last photo associated with a particular visit are assumed to represent the period that the camera was active thus the recommendation that cameras be triggered in the field when set checked or pulled In most cases these should be accurate but before performing any serious occupancy analysis you should double check to make sure none of the dates need to be modified Instructions on changing the active dates will follow after a few examples One case where you should modify the active dates is when the camera did not take photos of the crew who set checked or pulled it For example if a camera was set on June 1 at noon but didn t take a picture until the next day you can be reasonably certain it was working from the time it was set In this case you would change the start date for that visit to June 1 at noon Similarly if the camera wa
41. include species with identifiable markings and you want to run Mark Recapture analysis on your results you need to assign individual IDs to your photos first The first step is to identify sequences of photos that represent independent detections Start by clicking the Assign Individual IDs button on the Switchboard form If you haven t already done so you ll be prompted to automatically assign independent detections and a pop up form will appear Figure 18 you can access this form later on from the link on the IndividuallD form 5 AddindDetections Assign Independent Detections Select the species to update Canada Lynx Include Verified detections only C Pending and verified detections Number of minutes between independent events i60 nme Figure 19 Assigning Independent Detections Select the species in which you re interested identifying individuals and specify a time interval for creating independent detection events hereafter events The time interval represents the minimum time elapsed between consecutive events of a particular species at a given location that should be considered independent In other words if you select cougar in the drop down and enter 90 in the time interval field an independent event will be added for a photo of a cougar at Location X if at least 90 minutes have passed since the last photo of a cougar at Location X Independent events can be modified through the Individ
42. mageDate FileName FilePath Highlight VisitID 4 ills gt IndependentDetectio Y IndDetectionID SpeciesID LocationID DefaultStart ModifiedStart Deleted IndividualDetections Vm IndDetectionID IndividualID Comments Figure 26 Relationship schema A COLORADO Parks and Wildlife Department of Natural Resources Page 43
43. of Natural Resources To modify active dates for several visits open the OccupancyQueryBuilder form and click the View Edit Active Dates link Figure 23 As before the dates appear in red if they have been modified black if they still match the first and last photo Dates in red can be reset to the default by clicking the Default link to the right of the record E8 EditactiveDates x JJ Periods y s Visit Date c Active Comments Molas Pass Cam et 12 14 2013 pores jem E a MI Molas Pass Cami pun 2 8 2014 1 16 14 20 21 38 2 8 14 13 04 22 Molas Pass Cami0 set 12 19 2013 IL Molas Pass Cami0 Check 1 14 2014 12 19 13 16 28 13 1 14 14 14 24 10 Molas Pass camio Pull 2 9 2014 1 14 14 14 28 08 2 9 14 16 37 26 Molas Pass Camii set 12 19 2013 If Molas Pass Cam1i check 1 14 2014 12 19 13 17 26 34 1 14 14 15 00 52 Molas Pass Camii Pun 2 9 2014 i 14 1415 0726 2 9 14 16 12 46 Molas Pass Cam2 set 12 17 2013 IE Molas Pass Cam2 Check 1 14 2014 12 15 13 14 03 44 1 14 14 16 08 26 Default Molas Pass Cam2 Pull 2 8 2014 1 14 14 16 13 10 2 2 14 1 19 01 MolasPass Cam3 iset 12 14 2013 Moss ami Gea vhwam ajaa azza Visas MolasPass Cama Pun 2 8 2014 1 15 14 20 36 40 2 8 14 15 37 12 Molas Pass cama Set 1
44. oking through the photos via a thumb drive ftp site etc The person who uses the module can store it wherever they want it s perfectly fine to run it from a thumb drive or they can copy and paste the folder to any location on their computer The only caveat is that the folder must be copied in its entirety meaning the folder with the photos in it and the runtime database must be kept in the same location All of the information about trusted locations above applies to modules as well There is no built in way of keeping track of which photos you ve distributed and to whom creating a simple spreadsheet is recommended COLORADO Page 20 Parks and Wildlife Department of Natural Resources AG Photo ID Observers An appropriate standard for analyzing camera trapping data is to have at least 2 independent observers review each photo and the database is designed with this in mind There are really only 2 steps that need to be completed in this process first the photos must be reviewed by 2 observers and each observer must independently assign species to the photos Second a referee must compare any IDs that don t match between the 2 observers The referee can be one of the 2 observers who assigned species IDs or a third independent observer When you assign a species to a photo through the PhotolD form you re actually adding a new record to a table called Detections The ID associated with whichever observer is logged in
45. only support a certain number of files within a given folder and the limit has nothing to do with available storage space Our tests put this limit around 15 000 files but if you use very long filenames the limit could be significantly lower For most cases storing one memory card worth of photos per folder seems to work well but if you use very large memory cards it may be necessary to divide the files into smaller batches before importing them Of course it s always a good idea to maintain backup copies of the photos as well organize these however you want but save them on a different hard drive The recommended work flow would be something like this collect the memory card gt copy the photos to a backup folder gt import from the card to the database with the copy option selected details later gt format the memory card so it is ready to be cycled back into use A COLORADO Page 6 Parks and Wildlife Department of Natural Resources The Switchboard Form The form displayed when you first open the database Figure 3 is designed to allow users to perform most database functions without having to master the inner workings of Access Click on any of the buttons on the left to perform the action listed Most of these buttons open new forms which allow entering or viewing data importing photos viewing photos etc You can also exit Access by clicking the button next to Quit E Switchboard CPW Photo Warehou
46. ould have elapsed but if the camera didn t take photos before or after the check you may want to modify one of the active dates to make sure the camera is considered active the entire time To modify the active dates when necessary you have two options you can use the link on the Visits form or the link on the OccupancyQueryBuilder form Working through the Visits form Figure 22 is a little more error proof since you can only edit the dates for one visit at a time Simply navigate to the visit in question and click the link to open a popup form with the active dates The dates of the first and last photo are also listed for reference Any date en COLORADO Page 33 Parks and Wildlife Department of Natural Resources that has been changed will show up in red dates in black are set to the default first last photo value If you modify a date and change your mind you can just copy and paste the date from the first or last photo field Camera Visits Select a Location T Lizardi Visit Type pi 7 Visit Date 1 15 2014 Comments Photos Active Start 1 10 2014 12 27 01 PM Active End 1 15 2014 3 35 08 PM First Photo 1 10 2014 12 27 01 PM Last Photo 1 15 2014 3 35 0 enoto M 10f65 gt io Filter search 7 Access Somewhere near Telluride Figure 22 Editing active dates from Visits form COLORADO Page 34 Parks and Wildlife Department
47. pecies When adding a new detail item to the list you must specify the species to which that item applies Details and their shortcuts can be repeated for different species To use one of the examples above you could add collared as a detail that would apply to bobcats with a shortcut of C and then add it again with the same shortcut for mountain lions If you decide to skip steps 3 and 4 for now you can add species and details one at a time through the PhotolD form or you can edit the lists by selecting the appropriate option on the startup form Species 28k mune IS List e Detection Details List lc G 5 S Short N 5 1 Common Name Gent Species Shortcut Short Name Species Detail American Marten Martes lameri Marten Canada Lynx Collared Canadatynx canadensis E Lynx Canada Lynx Uncollared Coyote Cani latrans Coyote Human x LynxRec Crew Dog i Dog Red Fox gt Collared Gray Jay lf Gray Jay Great Horned Ow E sHow Human Homo sapi Human Magpie P___ Magpie Mountain Chickadee li MOCH Northern Goshawk l Noco Red Fox Vulpes vulpes Fox Red Squirrel Il I j Red Squirrel Short tailed Weasel Snowshoe Hare Unknown Figure 7 Adding species Figure 8 Adding details A
48. pile from the Debug menu If none of these fixes the problem your database is probably corrupted It may be fixable but will probably require expert attention Limitations Access databases can only handle 2 million rows in a single table which can be problematic when working with camera data Because the CPW database maintains records for multiple detections per photo you will most likely approach this limit when you have around 1 million photos There are some potential workarounds to this issue including permanently deleting duplicate detections but if you anticipate collecting more than a million photos you may want to look into more powerful database options such as Microsoft SQL Server Access databases are also limited to 2 gigabytes in size but in practice your database should never come close to this limit If you notice the file getting inexplicably large follow the steps above to compact and repair it COLORADO Page 9 Parks and Wildlife Department of Natural Resources A Using the Database Access databases are designed so that users interact with the data through forms rather than working directly in the tables All of the basic tasks required to catalog and identify your photos can be accomplished through forms which can be accessed using the options on the Switchboard form If you ve already closed it you can access most of the forms listed below by double clicking on the form s name in the navigation pane
49. re correct just delete the incorrect ones Having duplicate correct IDs is totally fine those photos won t appear next time you compare IDs Your goal is to remove any IDs that are incorrect not necessarily to narrow the list to a single record You may however run into situations where a single photo has multiple non matching IDs and all the IDs are correct meaning there is no record that needs to be deleted This can arise when more than one species is present in a photo for example In this case click the button labeled Verify All Species This will mark all of the records in the subform verified so that they won t reappear when comparing IDs later on If you accidentally delete the wrong record when comparing IDs you can press the Reset button which will set all of the detections for that photo back to pending If both initial observers were incorrect it is best from a bookkeeping perspective o add a 3 record for the correct species then proceed to delete the previous 2 records COLORADO Page 25 Parks and Wildlife Department of Natural Resources Using the PhotoViewer form Once you ve identified the species in your photos through the PhotolD form you can use the PhotoViewer form Figure 18 to view your photos and perform several additional actions This form contains more sophisticated filtering options for reviewing your photos in more meaningful groupings It also allows you to move through the photo
50. reating a Query with Photo Data From the PhotoViewer form you can create a query that will return the metadata for all of the photos that match your current filters You can then write additional queries on these results or paste the results into Excel for further analysis To do this specify the filters you want in the PhotoViewer form and then click the View Query Results button This will overwrite the query in the database called PhotoViewerQuery and the results will appear on screen This query returns location and date time data but it doesn t include species or details assigned For example if you wanted to examine changes in ungulate activity over time you could filter PhotoViewer to include only ungulate species click the button and export your results into Excel to create a graph Copying Photos Another button at the bottom of the PhotoViewer form allows you to copy photos based on your current filter settings Clicking this button opens a simple form where you can specify a destination folder for the copied photos and set renaming options similar to those on the ImportOptions form Before this form opens the PhotoViewerQuery is overwritten to reflect the current filters just as if you had pressed the View Query Results button and this query is then used to identify which files to copy A couple examples will make the purpose of this button clearer Say you deployed a camera on private land and the landowner requested
51. ree options you can delete the records for those photos from the database you can delete both the records in the database and the associated jpg files or you can switch the photos over to a different visit A COLORADO Page 13 Parks and Wildlife Department of Natural Resources Delete Visit There are photos associated with the visit you chose to delete What do you want to do with the photos C Delete records and jpg files C Assign the photos to a different visit r Figure 11 Deleting a visit with photos A few examples should make the options more clear If you associated a set of photos with the wrong visit but don t need to change the filenames the easiest fix is to delete the incorrect visit and assign the photos to the correct one If you haven t entered data for the correct visit yet you can delete the visit and the photo records but keep the jpg files That way once the correct visit is entered you can import those jpg files without copying them again If you re in a similar situation but you also renamed the photos while importing them and the names are incorrect you could delete both the records and the jpg files then redo the import using backup copies of the photos Likewise if you ve imported photos for a visit but then decide that all of them need to be excluded for some reason e g the camera was mounted upside down you can delete the visit along with all the records and jpg files and p
52. retend it never happened COLORADO Page 14 Parks and Wildlife Department of Natural Resources A9 Importing Photos Pressing the Load Photos button opens the ImportOptions form Figure 12 which is also available from the Switchboard form by pressing the button next to Import Photos In general it s better to import through the Visits form because the likelihood of assigning photos to the wrong visit is much lower especially if you have lots of locations or visits The ImportOptions form allows you to browse to a folder that contains jpeg images select the appropriate visit and import all of the photos in that folder into the database If you open it from the Visits form the visit will already be selected for you Importing doesn t necessarily entail moving the image files themselves at a minimum the data from the files is added to the Photos table in the database If you want however you can copy the photos to a new location in the same step this is particularly useful for importing photos directly from memory cards Make sure not to confuse the destination folder with the source folder There is a checkbox to include all subfolders within the source folder you selected especially helpful for importing from memory cards you can browse to the drive letter for the card and check the box to import everything on the card and there are a variety of options for renaming the files if you choose to copy them Af
53. s checked June 10 at noon but no photos of the field crew were taken the end date would be the date of the last photo As long as you re reasonably sure the camera was still operational when checked you should change that end date to June 10 at noon On the other hand a camera may continue to take photos even though it doesn t meet your standards of functionality If you use bait for your sets and the bait is removed by scavengers you may want to consider changing the end date for that visit to reflect when the bait disappeared If a camera is disturbed by a bear and ends up pointing at the ground it may still take a few pictures but obviously it isn t as likely to detect wildlife as it should be so you would set the end date to whenever the disturbance occurred In some situations involving camera failure you don t need to worry about changing the active dates This is the case when the camera fails in a way that prevents it from taking photos after the fact such as battery failure or running out of storage space on a memory card In these situations the date of the last photo is an accurate representation of when the camera stopped functioning One other important point a camera is considered continuously active across a check visit if less than 12 hours elapse between the active end of the earlier visit and the active start of the second visit Assuming the crew checking the camera triggered it as they arrived and left only a few minutes sh
54. s more easily than PhotolD The location season and species filters for this form are dependent so you can t select a particular season and then select a location that doesn t have any images for that season for example Other filters are not dependent so you may filter down to zero photos when you use those If you want to include photos for some species but not others use the Multiple Species button to open a form in which you can select the species you want to include Like PhotolD PhotoViewer can advance through photos automatically Filters Field Season 1 rj Highlights only Time E Image Data Date 2 18 2014 UTM E 244444 UTM N 4184444 Edit Species ID Copy Photos View Query Results Delete Photos Species Canada Lynx Uncollared 1 Advance Automatically Figure 18 PhotoViewer form PhotoViewer also contains a section that displays all of the additional data for each image in the lower right corner If you need to edit the species for a photo from PhotoViewer press the Edit Species ID button This simply loads the current image into the PhotolD form in a pop up window This is not an effective way to assign species IDs for batches of photos since only one photo is loaded at a time Additional actions you can take from this form are detailed in separate sections below COLORADO Page 26 Parks and Wildlife Department of Natural Resources C
55. s of unexpected results even if you don t intentionally change anything COLORADO Page 4 Parks and Wildlife Department of Natural Resources AG Pu Microsoft Access e El 5 0 Home Create External Data Database Tools H d ee HE MES 33 Copy m cim View Paste B z u A 5 E8 J Format Painter Views Clipboard i Font Security Warning Certain content in the database has been disabled Options VBA is currently disabled To use the Da the options button c To avoid this in the future create a Trust save the dat Figure 1 Access window with code enabled Figure 2 Access window with code disabled You can click the Options button below the ribbon and enable VBA in the dialog box that follows but you ll have to do this each time you open the database and you may receive confusing security messages while using the database A better way to ensure that code in the database isn t blocked is to save it in a Trusted Location First open Access from the start menu You should see a welcome screen with options to build a new database open an existing one get content from Microsoft Online etc Click the Office Button Now click Access Options Trust Center gt Trust Center Settings Trusted Locations Check to see if the folder where you want to save the database is included in the list If not you can add it by
56. se Figure 3 Switchboard form This form contains the code that hides the ribbon and navigation pane on startup If you close the form by clicking the red X at the top of the form window not the one at the top of the screen which closes Access completely the ribbon and navigation pane will appear This allows you to make design changes to the database create new queries etc If you ve closed the form and you want to get back to it all you have to do is open it by locating the form named Switchboard in the navigation pane and double clicking it More detailed information about each of the commands can be found in the relevant sections below COLORADO Page 7 Parks and Wildlife Department of Natural Resources The Navigation Pane When the Switchboard form is closed the navigation pane appears with the view set to Custom Figure 4 in which objects are grouped in simplified categories Many of the lesser objects subforms subreports etc are filed in hidden groups To change the navigation pane view click the drop down arrow at the right of the title bar In the menu that appears you can select from a variety of viewing options Object Type can be useful Developer is a more advanced custom option Most of the objects that are hidden from the custom view are hidden for a reason you can seriously impair the functionality of the database by modifying these objects If you re an expert in Access
57. study areas and deployment periods into a single grouping variable The first deployment period at a given location is represented by the study area name followed by a 1 and subsequent deployments will be numbered sequentially For MARK input files the session is identified using group variables after the capture history There may be times when you need to change the session field manually after exporting your data to achieve the correct grouping For example imagine our study area is Telluride and it contains camera locations numbered from 1 to 20 In 2013 cameras were set at locations 1 to 10 and in 2014 cameras were set at all 20 locations If you don t filter by year when creating files for R or MARK the first session will contain 20 deployments because it s based on when a camera was first set at a particular location The 10 cameras set in 2013 and the 10 cameras set at new locations in 2014 will be grouped together in the session Telluride1 The session Telluride2 will contain the 2014 data for locations 1 to 10 since 2014 is the second deployment at those locations To group your data more logically you would need to update the session to Telluride2 for locations 11 to 20 and adjust the detector files accordingly Another option would be to filter by year when creating your mark recapture queries to ensure the deployments are grouped correctly but this approach will fail if you have more than one deployment per year SECR analysis requires
58. ter you ve imported photos for a visit the Load Photos button will be replaced with the images themselves If you need to import more photos for the same visit for example if you have paired cameras at each location you can move past the last photo in the subform and the button will reappear You can also add additional photos by clicking the Import Photos option on the Switchboard form then clicking the link to show visits with photos Camera Visits isit for the photos you want to import r Lizardi 1 15 2014 Pull Enter the path for the folder containing the photos G V Include subfolders V Copy image files Destination folder F SampleProject Photos Lizard1 Rename image files Prefix Options Location ID Text Prefix Prefix T Lizard1 Rename files using C Image Number Date Time C Image Number Date Image Number Number of digits for image number Figure 12 Importing photos COLORADO Page 15 Parks and Wildlife Department of Natural Resources A Identifying Species Use the ID Photos command from the Switchboard form to open the PhotolD form Figure 13 Before the form opens you ll be prompted to log in If your name isn t already in the list just type it in and hit Enter then you ll be prompted to add some additional contact info optional Never log in as someone else to ID photos
59. tered Once you ve entered data for a check or pull visit a button will appear in the lower part of the form that allows you to import photos for that visit Figure 10 Camera Visits Camera Visits asma Photo K saoti M Somewhere near Telluride 3 Somewhere near Telluride Figure 9 Visits form Set Figure 10 Visits form Pull Visits are relatively straightforward but there are a few things to keep in mind when entering this data Don t try to represent problems with the cameras by altering your visit information There is a better way to indicate issues such as battery failure or camera disturbance more on that later If you retrieved a camera on June 1 and realized it hadn t been working properly as of May 15 your pull visit should still be entered as June 1 There is no limit on the number of visits of any type for a given location If you set up a camera at the same location in two different years that should be entered as a single location with 2 sets one in each year 2 pulls and unlimited checks in between Photos are always associated with the visit when they were collected check or pull visits If you need to delete a visit you can do so by clicking the Delete button If there are already photos associated with the visit you wish to delete you ll have to decide what to do with them A popup form Figure 11 allows you to choose one of th
60. the left the currently selected photo and a subform for adding individual IDs in the center and a few options for modifying events and viewing reference photos on the right The filters across the top of the form work similarly to those in the PhotolD form View reference photos for Edit Detection Event Detection event H 4 4of7 Figure 20 IndividuallD Form Note that while this form appears superficially similar to the PhotolD form it is different in some important aspects Each page in this form represents a single indepedent event A COLORADO Page 29 Parks and Wildlife Department of Natural Resources consisting of a sequence of photos filmstrip on left of one or more individuals of a given species at a given location To move between events use the navigation bar at the bottom left Add individual IDs for the current event using the subform at the bottom which works just like the one on the PhotolD form Once you ve added an individual ID a link will appear that you can use to set a reference photo for the individual in question Unlike the PhotolD form it s not important which individuals are in which photos the individual ID applies to the collection of photos Just enter all of the individuals present in the sequence in the subform When assigning individual IDs you should always check through all the photos on the left side of the form
61. tion name will appear light green and when all of the photos in a group have verified IDs the location name will appear darker green The Observer Comparison report is provided to give you an idea of how different observers are doing with regard to identifying species in photos If you ve assigned individual IDs in addition to species you can open the Individual Detections report to view a list of detection events and the individuals assigned COLORADO Page 41 Parks and Wildlife Department of Natural Resources A Tables The tables are described here mainly to provide insight into the functioning of the database Working with the data in the tables directly is never a good practice whenever possible use forms to access the data The CameraLocations table lists each of your camera locations with UTMs and optional access information Each location is associated with a study area via the StudyArealD field which corresponds to the field of the same name in the table StudyAreas where the study area names are stored You can t enter a StudyArealD that doesn t match an existing record in the StudyAreas table so you have to add at least one study area to that table before you can enter location records The Visits table contains a record for each time a camera was set checked or pulled The LocationlD field relates Visits to the CameraLocations table The type of visit set check or pull is represented by an integer in the
62. tiple photos at once by pressing the Batch ID button on the PhotolD form This will bring up a new form Figure 14 Use the drop down on the left to select the first photo in the series and the drop down on the right to select the last Enter the data you want to add for this range of photos in the bottom of the form and click Apply If you ID the photo first in the PhotolD form and then click the Batch ID button the ID info will be filled in for you Be judicious when using the batch ID feature it can be a lifesaver when you come across a thousand photos with nothing in them but it also makes it easier to miss something important It s generally most useful for those who like to flip through their photos in Windows Photo Viewer or another photo viewing program while ID ing them If you prefer this method enter an ID for a photo and double click the photo to open it in Windows Flip through until you find the last photo with the same content return to the database and click the Batch ID button Finally select that final photo on the right side of the BatchID form and click apply Last Image T Ophirl 03447 jpg ID to apply Species Detail Individuals OITBINENENENNNENEEBSNS Lynx iUncollared a Figure 14 BatchPhotoID form COLORADO Page 19 Parks and Wildlife Department of Natural Resources Distributing Photos for Others to ID One of the biggest advantages of this databas
63. to ensure that no additional individuals are present and that they were grouped correctly If not use one of the buttons on the right to adjust the detection event as follows Delete This button will delete the current event Photos currently loaded in the film strip will be considered part of the previous event for this location This button is unavailable if there are no previous events for the current species at the current location Split This button will create a new event starting with the currently selected photo Use it if you feel that the photos on the left represent two independent events instead of one Unavailable if the current photo is already the start of a detection event Adjust Start Time This button opens a pop up that allows you to select the first photo for the current event Use it if the first few photos loaded on the left should actually be part of the previous event or if the last few photos for the previous event actually belong with this one Unavailable if the current photo is already the start of an event Pay special attention to events with more than one individual it can be tough to decide when they should be grouped as a single event or split into two In general if it seems like the animals are moving together they should be grouped together but if one individual leaves as soon as another arrives the events should probably be considered independent You can view reference photos for a particular individual by
64. ttings and filters will be added to a separate sheet within the workbook You can also open your query results in a new tab but you can t save queries built with this form Instead you can preview your results in a snappy chart Figure 25 only available when the output format is set to decimal days COLORADO Page 37 Parks and Wildlife Department of Natural Resources AG Activity Data E American Marten Zone 1 Bl Red Squirrel Zone 1 L1 Snow shoe Hare Zone 1 gt U c v J c KH hee ire 0 SPS AMO S OS S SSS GU dv KK de XS XY AW we S v Time Figure 25 Activity Data Chart COLORADO Page 38 Parks and Wildlife 7 Department of Natural Resources Mark Recapture Analysis A third query builder form is available for creating mark recapture input files for program MARK or the R package secr to open it click Build a Mark Recapture Query on the Switchboard form In order to run either analysis on your data you need to first identify individuals in your photos see the Identifying Individuals section above The start date options filters and buttons all work exactly as they do on the occupancy form Interval options are similar but no buffer period is available because results are based on independent detections rather than individual photos There is no option to require two observers because observers are not recorded when assigning individual IDs The Session field in secr queries combines
65. uallD form if A COLORADO Page 28 Parks and Wildlife Department of Natural Resources they don t turn out exactly right so don t stress too much about what you decide to use For most species 60 minutes will work fine Note that this structure is a departure from how identification of species was handled in the database For species ID an observer reviewed every photo and assigned one or more species to that photo Here an observer assigns an individual ID to each event which is often a collection of photos This structure improves the efficiency with which individual ID data can be stored and manipulated behind the scenes Furthermore it improves the efficiency with which individual IDs can be assigned as a single ID will be associated with a potentially large collection of photos from the same event rather than with each individual photo Thus the observer is relieved from unnecessary repetitive ID work In general it s best to have all of your species assigned and reviewed before you assign independent events in which case you can leave the option to include verified detections only set On the other hand if you have still have pending IDs in your Detections table you may get better results if you select the option to include them Once independent events have been assigned you can move on to identifying individuals using the IndividuallD form Figure 19 This form displays a series of photos film strip style on
66. w don t select it Press ctrl C to copy the selected cells then move back to the form in Access Click the blue box to the left of a new record so that it turns black then press ctrl V to paste your records You will probably get an error message about control names not matching it s okay to dismiss this message and continue the paste operation If you get any other error message you should cancel the process and enter your locations manually COLORADO Page 11 Parks and Wildlife Department of Natural Resources AG The third and fourth steps are not required for importing photos but it makes sense to spend a little time on them now to make things work more smoothly later on Step 3 is to add a list of species you expect to detect to the Species table Figure 7 Switchboard gt Edit the Species List An entry for None meaning no species is present in the photo has already been entered for you but it won t show up in the form As you enter additional species you can assign keyboard shortcuts for use when ID ing photos and a shorter name that will be used in drop down menus where space may be limited e g Lynx for Canada Lynx Step 4 is to do the same with detection details Figure 8 Switchboard gt Edit Species Details which requires some explanation Detection details provide a little more specificity to detection records Examples would be on leash for a dog or collared for wildlife s

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