CAPS-IBI Users Manual 1.0
Contents
1. 42 304100 OEE RESULT To ternar _ReroRT 1 G25_MAP CHECK True THAP CHECK dar 12 passed the checking process ove Figure 6 A Sample Project File As seen in Figure 6 Project 9 ibi has a CSV Data File stored in C download TestAbundanceData_fixed csv but it does not have an Error Report file because the CSV Data File passed the checking projects as described on the DATA_CHECK_RESULT line and as mentioned above the error report file is automatically deleted once the CSV data file has passed the checking process Because project 9 ibi has successfully passed all the steps needed to calculate the IBls the project probably also has a calculation results file 9_calc_results csv stored in the same directory as the project file If project 9 ibi had a 9_error txt file it would also be stored in the same directory as the project file We have not included a menu option for deleting a CAPS IBI project because of the several possibilities for which files you may want to save or delete For example you may want to keep the 9_calc_results csv file for later comparison but delete any ather files associated with the project We also have not included the option to rename a project because we would have to ask whether you would like to save the old project or perhaps delete only certain files in the old project Also having several files that use the same CSV data file migh2. click the file to open the install wizard and then follow the instructions We recommend installing the software using the default settings For windows users the default installation will create a folder in the program files list and the program can be opened just like any other Windows program CAPS IBI is written in the Python programming language and makes use of the Quantum GIS API and the Inno Setup 5 installer program Who should read this manual We hope that all users of the software will read this manual carefully The CAPS IBI software appears fairly simple on the surface but a lot is going on internally that is nat obvious in the graphical user interface GUI Glossary of Terms Term Definition Action The function performed by clicking a button or choosing a menu item Compliance Level There are three possible results Exceeds expectations Meets expectations or Fails to meet expectations Comma Separated Value CSV data file The file that contains the biological sampling data see Step 4 below for format IBI Metric See http www umasscaps org edf CAPS Landscape Metrics pdf for individual metric definitions IBI Score The score calculated by statistical modeling based on the field collected biological data 18I Table The table that appears in the main window when CAPS IBI is opened Metric Type Either Stressor or Integrity Resiliency see http ww
3. CAPS Conservation Assessment and Prioritization System lt 27 CAPS IBI User s Manual Version 1 0 July 2015 UMassAmherst Preface Acknowledgements Funding for the development of CAPS IBI was provided by the Massachusetts Department of Environmental Protection and the U S Environmental Protection Agency under section 104 b 3 of the U S Clean Water Act Thanks to the R Project for Statistical Computing the developers of the Python programming language and the QT Project for making their excellent open source software available to all License of this document Permission is granted to copy distribute and or modify this document under the terms of the GNUFree Documentation License Questions and Comments Technical Support Questions about CAPS IBI Bob English Daystar computing and research services 367 Four Mile Brook Rd Northfield MA 01360 Phone 413 834 1841 Fax 978 882 0243 bobengl gmail com http edaystar com Questions about the Conservation Assessment and Prioritization System Scott Jackson Dr Kevin McGarigal Department of Environmental Conservation Department of Environmental Conservation Holdsworth Hall Holdsworth Hall University of Massachusetts University of Massachusetts Amherst MA 01003 Amherst MA 01003 Fax 413 545 4358 Phone 413 545 4743 Fax 413 545 4358 Phone 413 577 0655 Email sjackson umass edu Email megarigalk eco umass edu Links More informat
4. ae FIGURE 4 Proper CSV Data File Format Figure 4 above shows an example of the CSV file format that must actually be submitted The first line has the column names separated by commas As illustrated by the column name line there is no comma after the last item in the line if all columns have a value In other words there should be 9 commas delineating the 10 possible entries for each line Each line represents one record in the data set and missing items are indicated by adjacent commas Note that each line ends with a carriage return but if you open your CSV file in a text editor the carriage return markers may or may not show depending on your text editor settings There cannot be any carriage returns before the column names or after the end of the last line or record Lastly you should not use commas within an item say a site name containing a comma If you must use commas within your text please learn how to delimit the text properly or simply use Excel which will write the file properly for you The following bulleted list describes what errors CAPS 1BI checks for in the CSV data file Please note that the checking process is case insensitive Wetland type and sample type are required for all records The wetland type entries must be the same as the name of the wetland type you have selected The sample type must be one of the three entries shown in Figure 5 below The sample type must agree with the wetland typ
5. e you have chosen The taxa supplied for each record must be in the group specified for the sample type Site is required for all records and can be a number or a name as you prefer but it must be the same for all records Abundance is required for all records If species is indicated then genus must be supplied Otherwise listing a single taxon other than species genus family order class or division is sufficient and will pass validation The spelling of each taxon is checked against the built in database and must be correct If more than one taxon is listed for a record then the combination must be found in our database Once you have created a properly formatted CSV data file click the Browse button and browse to the file As soon as you have selected the file and clicked Open in the file dialog CAPS IBI will display the path to your file and automatically begin the process of checking for errors If CAPS IBI finds errors it will write an error message in red next to the Result of data check label and a new window titled Error Report will appear and describe the error and the line number for each error The program will also write an error file named yourprojectname_error txt to the same directory as the project file in case you choose to save the project and continue later The error file can be displayed at a later time by clicking the View Error Report button After you have fix
6. ed the CSV file a message in green text will appear next to the Result of data check label indicating that your data file has passed the check and the error file will automatically be deleted In addition a file named yourprojectname_completed_taxa csv will be written to the project folder with missing taxa information filled in for reference lsample type wetland type group vascular plants Forested wetland vascular plant bryophytes Forested wetland bryophyte kn invertebrates Stream macroinvertebrate Figure 5 sample type Step 5 Congratulations If you have successfully completed Steps 1 4 the Calculate button is enabled and you are ready to do calculations for your IBls If you click Calculate before you have saved your project you will be prompted to save the project before the calculations begin The calculations use the R Project for Statistical Computing software and consist of complex statistical modeling based upon the biological data you have submitted Once the calculations have completed the results will appear in the IBI Table and CAPS IBI will write the results to a CSV file named yourprojectname_calc_results csv SOME ADDITIONAL IMPORTANT INFORMATION As described above every project has a project file consisting of the project name and the ibi extension Figure 6 below shows the project file for 9 ibi daD raeh hs 2 1aTTTUDE
7. erations Imperviousness Nutrients Phosphorus Road Taffic Figure 1 The Main Window After opening the software for the first time the Main Window shown in Figure 1 will appear and you should begin by clicking the New Project button A file dialog will open that will allow you to save a project anywhere you choose on your file system After you name the project and click Save the program will automatically add the ibi extension to your file name and display the project name in the Main Window title bar Files with the ibi extension are simple text files that stare information about the status of your project 50 you can partially complete a project and then return to it later by using the Open Project button or menu item Immediately after saving your new project the Create IBI dialog shown below in Figure 2 will open This dialog is modeless which means you can select any of the menu items or buttons in the Main Window at the same time the Create IBI dialog is open As you can read in the green text just below the title bar this dialog asks you to complete 5 steps in order to be able to calculate results for an IBI The Calculate button at the bottom of the dialog will not be enabled until all 5 steps are completed without errors Note that the dialog displays the project name 9 ibi also in green text on the second line of text below the title bar The 5 steps displayed in Figure 2 a
8. in an area The first step in the CAPS approach is the characterization of both the developed and undeveloped elements of the landscape With a computer base map depicting various classes of developed and undeveloped land we then evaluate a variety of landscape based variables metrics for every point in the landscape A metric may for example take into account the microclimatic alterations associated with edge effects intensity of road traffic in the vicinity nutrient loading in aquatic ecosystems or the effects of human development on landscape connectivity Various metrics are applied to the landscape and then integrated in weighted linear combinations as models for predicting ecological integrity This process results in a final Index of Ecological Integrity IEI for each point in the landscape based on models constructed separately for each ecological community What is CAPS IBI Over the course of several years UMass Amherst has been collecting biological data in forested wetlands and using data collected by the MA Office of Coastal Zone Management and MassDEP in salt marshes and wadable streams These data were used to create and test Indices of Biotic Integrity IBIs for CAPS IEI and metrics CAPS IBI is software that allows cooperating agencies organizations and businesses to input field collected biological data and output IBI scores for IEI and some of the CAPS metrics for forested wetlands salt marshes or wadable s
9. ion about the Conservation and Prioritization System can be found at http www umasscaps org The Microsoft Windows CAPS IBI_1 0_setup exe can be found at https sourceforge net projects capsibi files The complete source code for CAPS IBI is available at https sourceforge net p capsibi code ci master tree Please report bugs or feature requests at https https sourceforge net p capsibi tickets A copy of the license for this manual can be found at http www gnu org copyleft fdl html Table of Contents Preface i Overview What is CAPS What is CAPS IBI How do I install CAPS 1B1 Who should read this manual Glossary of Terms How to Use CAPS IBI 3 The Project Menu Step 1 Step 2 Step 3 Step 4 Step 5 SOME ADDITIONAL IMPORTANT INFORMATION 7 Overview What is CAPS The Conservation Assessment and Prioritization System CAPS is an ecosystem based coarse filter approach for assessing the ecological integrity of lands and waters and subsequently identifying and prioritizing land for habitat and biodiversity conservation We define ecological integrity as the ability of an area to support biodiversity and the ecosystem processes necessary to sustain biodiversity over the long term CAPS is a computer software program and an approach to prioritizing land for conservation based on the assessment of ecological integrity for various ecological communities e g forest shrub swamp headwater stream with
10. land type are found the software then identifies the appropriate CAPS cell closest to your GPS point and indicates that the location is suitable If the location is suitable the software also displays the distance between your GPS point and the nearest suitable CAPS cell The box size is based on an assumption that GPS coordinates will be accurate to within 30 meters Step 3 Click the links below and check the boxes to confirm your sample location on a Google Map Once you have entered acceptable GPS coordinates CAPS 1BI will generate two blue colored links to Google Maps One link will display the location of your GPS paint and the other will display the location of the nearest CAPS cell for your wetland type We ask that you click on each link and verify that your GPS coordinates accurately represent the location where you took your sample A marker will appear on the Google map that indicates the location of your GPS coordinates or the location of the nearest CAPS cell depending on which link you have clicked The coordinates will either appear near the marker or in the search box of the map and the marker shape or color may differ depending on your operating system and or web browser Please note that you can change the map from a map view to a satellite image view if necessary After you have clicked a link the check box labeled GPS coordinates OK or Nearest point OK will become active You must check those checkboxes before
11. re described in detail below To create and calculate results for an IBI please complete the five steps below Project Mame o r step 1 choose a wetland type Step 2 tnter the GPS coordinates of your sample location in decimal geographic coordinates WOSO4 E Laude 6 gts from 41 2390 to 42 5860 __ Longte 6 digte from 73 5002 to 69 9278 _ ent of locaton chest Coordinates no antered vai Stop 3 ick the inks below and check the boxes to confirm your sample location on a Google Map Diepiay CPS pont 5 oat Display nearest point having IEI cauleton For your chosen wetland typa Stop 4 Browse to a Comma Separated Vale CSV le that contains your data Browse o mie seca Rasut of data check iw Error Raper Step 5 cick to calculate and display resus Figure 2 The Create IBI Dialog Step 1 Choose a wetland type The drop down menu shown in Step 1 has 3 choices Salt Marsh Forested Wetlands and Streams Currently we do not have credible IBIs for the Salt Marsh selection The wetland type must be chosen before entering GPS coordinates in Step 2 because CAPS IBI will check if your GPS coordinates are in a suitable location for the wetland type you have chosen The wetland type must also be chosen before choosing the Comma Separate Value data file in Step 4 because the software will check if the wetland type listed in the data file is consistent with
12. t be confusing So to entirely delete a project simply delete all of the 4 possible files associated with the project myproject ibi myproject_error txt myproject_calc_results csv and myproject_completed_taxa csv To rename a project open myproject ibi in a text editor and change the project name then rename the 4 files Using the new project name Alternatively you may rename a project by deleting the old project and creating a new project with a different name the process of creating an IBI is fairly quick and simple Finally we should describe the process that occurs when opening a previously saved project Because it is possible to hand edit or move any of the 3 files associated with a project the software always checks the files when the project is opened Because any of the 3 files may have changed we recheck the GPS coordinates the CSV data file and perform the calculations again depending on the status of the project when it was last saved You will be notified if the GPS coordinates or CSV data file have changed or if the CSV data file is missing Please be aware that the error report will be rewritten or overwritten as will the projects calculation results file and the Create IBI dialog will reflect the current state of the project If the CSV data file is missing you will be asked to relocate it We hope that you will find CAPS IBI to be a valuable tool that is easy to install and use If you have an
13. the wetland type you have chosen If you attempt to change the wetland type after you have entered GPS coordinates or chasen a data file a dialog will appear to warn you that you must also change GPS coordinates and your data file The dialog will give you a choice of whether to proceed or cancel If you proceed the coordinates in Step 2 ad the CSV file in step 3 will be reset to default values Step 2 Enter the GPS coore 4326 ates of your sample location in decimal geographic coordinates WGS84 EPSG The coordinates listed in parentheses after the Latitude label and Longitude label are the coordinates for the maximum extents of Massachusetts so your coordinates must be between those limits to be valid You also must enter 6 digits beyond the decimal place in order for the latitude and longitude text boxes to accept your entry as valid Once you have entered valid coordinates and hit the tab or enter key the software will check your GPS coordinates against a built in database of suitable locations for the wetland type you have chosen and will display green text indicating that the location is suitable or red text indicating that itis not suitable For those who are interested CAPS IBI constructs a box of suitable size around your GPS coordinates and finds any CAPS cells that fall within that box If no CAPS cells of the designed wetland type are found within the box then the location is not suitable If CAPS cells matching your wet
14. treams CAPS BI can be used to Evaluate the biological condition of particular sites and assess whether IBI scores meet expectations for wetlands in their specific landscape contexts Identify whether site specific stressors e g chemical dumping are affecting the biological condition of wetlands beyond the general stressors associated with the surrounding landscape e Assess progress and the success of wetlands mitigation projects Assess the impact of wetland restoration projects How do install CAPS IBI CAPS IBI currently is intended to run primarily on Microsoft Windows operating systems XP Vista and Windows 7 and Windows 8 although files are available that make it possible for very experienced computer Users to run the software on nearly any operating system Hardware requirements include a minimum of For information about IBI development see Empirically Derived Indices of Biotic Integrity for Forested Wetlands Coastal Salt Marshes and Wadable Freshwater Streams in Massachusetts available at http umasscaps org pdf CAPS 20IB1920Report 20Sept 2015 202013 20Final pd 512MB of RAM and about 300MB of free disk space Microsoft Windows users can download the standalone installer using the link found in the Links section above Please note that you must have Administrator privileges to install but once installed those with user privileges only may use the software To install just click or double
15. w umasscaps org pdf CAPS Landscape Metrics pdf Percentile The percentage of values that is expected to fall below the given value e g IBI score based on training data used to create the IBIs Target Score The expected IBI score based on the metric or IEI score calculated by the CAPS model for the CAPS cell nearest the GPS coordinates of the sampling site Wetland Type Currently users may choose among Salt Marsh Forested Wetlands or Streams How to Use CAPS IBI As seen in Figure 1 below the Main Window has a single menu named Project The project menu has three actions in it New Project Open Project and Save Project The buttons on the toolbar perform the same three actions as the items in the project menu You may notice that the Save button on the toolbar is grayed out which means it is not available to use The Save button is only available when there is something to save In Figure 1 looking below the toolbar you see the IBI Table When an IBI has been completed the calculation results will be displayed in the IBI Table Please note that the number of output metrics will vary depending on the wetland type being assessed Target Score BESET fromm CAPS Compliance Level Percentile Metric Type Ecological Integrity Ecological Integrity stream Habitat Loss Watershed Habitat Loss Road Sediment Comnectedness Invasive Earthworms Edge Predators Hyrologic Alt
16. y problems or have requests for additional functionality please submit a ticket using the link provided in the Preface section above Thanks Bob English and the CAPS team
17. you can proceed with your calculations Step 4 Browse to a Comma Separated Value CSV file that contains your data Probably the easiest way to create your CSV data file is to type the column headings and other data into separate cells in Microsoft Excel or Open Office Calc and then choose to save the file as a CSV file However the file can also be created in a text editor if you prefer If you do use a text editor please do not use Unicode encoding for your file however UTF 8 or ASCII will work fine An example for creating the CSV data file in Microsoft Excel is illustrated in Figure 3 below wetland typelsample type site abundance genus ispecies emily order dass avision streem __ kn invertebrates 1 10Campeloma streem Jen invertebrates 11 10 Campeloma streem Jin invertebrates 11 4 Naididae Stream un invertebrares 1 6l Tubificida streem kninvertebrates 11 sl Citetiaa Stream kn invertebrates 11 6l Arthropoda Figure 3 Create Data File using MS Excel wetland type sample type site abundance genus species family order class division Stream kn invertebrates 1 10 Campeloma Stream kn invertebrates 1 10 Campeloma Stream kn invertebrates 1 3 Hydrobiidae Stream kn invertebrates 1 8 Pseudosuccinea columella Stream kn invertebrates 1 3 Planorbidae Stream kn invertebrates 1 3 Planorbid
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