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SDMtoolbox User Guide By Jason L. Brown, The City College of New York Last upda

SDMtoolbox User Guide By Jason L. Brown, The City College of New York Last updated: 10/14/2014 The SDMtoolbox consists of a series of python scripts designed automate complicated ArcGIS analyses that are often too difficult/tedious for the average GIS user to execute efficiently. This tutorial gives a basic introduction to use SDMtoolbox for ecology and evolution studies. A large set of the tools here are designed to complement MaxEnt species distribution models (SDMs) or to improve the predictive performance of MaxEnt models. The MaxEnt program uses maximum entropy modelling of species’ geographic distribution (Phillips et al. 2006) and has become one of the most prevalent methods due to its high predicted performance, computational efficiency and ease of use. Many of the analyses are also available for use on other SDM methods (see: SDM Tools 1. Universal Tools). If you use the SDMtoolbox please remember to cite it. By citing this you encourage the development of more tools. Please use the following reference: Brown, J.L. (2014) SDMtoolbox: a python‐based GIS toolkit for landscape genetic, biogeographic and species distribution model analyses. Methods in Ecology and Evolution Table of Contents Getting Started ............................................................................................................................................. 5 Downloading ............................................................................................................................................. 5 Installation ................................................................................................................................................ 5 Uninstalling or updating ..……………………………………………………………………………………………………………………6 A First Run ................................................................................................................................................. 7 Analyses Guide ........................................................................................................................................... 10 Chapter 1. Biodiversity Measurements ..................................................................................................... 12 Estimate Richness and Endemicity (WE and CWE) ................................................................................ 13 ARCGIS STEP‐BY‐STEP GUIDE: ................................................................................................................... 13 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ......................................................................................................... 14 Results ................................................................................................................................................. 15 Chapter 2. Landscape Connectivity ........................................................................................................... 18 Landscape Connectivity .......................................................................................................................... 19 ARCGIS STEP‐BY‐STEP GUIDE: ................................................................................................................... 19 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ......................................................................................................... 21 Results ................................................................................................................................................. 23 Chapter 3. Species Distribution Modeling Tools ....................................................................................... 24 Correcting Latitudinal Background Selection Bias ................................................................................ 24 Solution 1 ................................................................................................................................................ 25 Tool: 1. Bias File for Coordinate Data (BFCD) in MaxEnt .................................................................. 25 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 25 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 26 Tool: 2a. Background Selection: Sample by Buffered MCP .............................................................. 27 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 27 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 27 Tool: 3. Clip BFCD by BS Bias File ....................................................................................................... 28 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 28 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 28 Solution 2 ................................................................................................................................................ 29 Tool: 1. CSV to EAP. MaxEnt format output (runs both 1a and 1b) ................................................. 29 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 29 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 29 Tool: 2. Project Climate Data (Raster) to Equal‐Area Projection (Folder) ........................................ 31 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 31 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 31 Distribution Changes Between Binary SDMs ......................................................................................... 32 Tool: Centroid Changes (Lines) .......................................................................................................... 32 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 32 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 33 Tool: Distribution Changes Between Binary SDMs ........................................................................... 34 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 34 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 34 Results ............................................................................................................................................. 35 Overprediction Correction: Clip Models by Buffered Minimum Convex Polygons ............................... 36 Tool: Binary Models (folder) .............................................................................................................. 36 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 36 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 37 Results ............................................................................................................................................. 38 Tool: Continuous Models (folder) ...................................................................................................... 39 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 39 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 39 Results ............................................................................................................................................. 40 Background Selection via Bias Files ....................................................................................................... 41 Tool: Background Selection: Sample by Buffered MCP .................................................................... 42 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 42 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 43 Tool: Background Selection: Sample by Distance from Obs. Pts. ..................................................... 43 ARCGIS STEP‐BY‐STEP GUIDE: ............................................................................................................... 43 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ..................................................................................................... 44 Create Friction Layer: Invert SDM .......................................................................................................... 44 ARCGIS STEP‐BY‐STEP GUIDE: ................................................................................................................... 45 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ......................................................................................................... 45 Results ................................................................................................................................................. 46 Spatially Rarefy Occurrence Data….…………………………………………………………………………………………………45 ARCGIS STEP‐BY‐STEP GUIDE:.…………………………………………………………………………………………………………….46 SDMTOOLBOX STEP‐BY‐STEP GUIDE:..…………………………………………………………..………………………………………46 Chapter 4. Basic Tools: Raster, CSV & Shapefile tools .............................................................................. 50 Tool: CSV to shapefile ............................................................................................................................. 50 ARCGIS STEP‐BY‐STEP GUIDE: ................................................................................................................... 50 SDMTOOLBOX STEP‐BY‐STEP GUIDE: ......................................................................................................... 50 Chapter 5. Running a SDM in MaxEnt: from start to finish ..................................................................... 51 Data Preparation ................................................................................................................................ 51 1. Preparing Worldclim Data ……………………………………………………………………………………………… 51 2. Testing Autocorrelations of Environmental Data…………………………………………………...…………54 3. Preparing Occurrence Data…………………………………………………………………………………………..… 55 4. Creation of Bias Files……………………………………………..………………………………………………………… 62 Model Creation, Calibration and Evaluation………………………………………………………………………………..64 5. Spatial Jackknifing …………………………………………………………………………………………………………….64 Getting Started Downloading The latest version of the toolbox is available for download at: www.sdmtoolbox.org. This software requires ArcMap 10.1 or 10.2 with an active Spatial Analyst license (www.ESRI.com). This toolbox is programed specifically for ArcMap 10.1 (and above) and due to a series of improvements in this version, it is not backwards compatible with older releases of ArcMap (i.e. ArcMap 9.2). This software consists of an ArcGIS toolbox and associated python scripts. Installation 1. Download, unzip ‘SDMtoolbox.zip’ and place all files in a folder on your harddrive where you want the toolbox to be stored (e.g …\Documents\ArcGIStoolboxes) 2. Close all ArcGIS programs 3. Open ArcCatalog 10.1 (a program in the ESRI ArcGIS programs, see icon below) Above: ArcCatalog Icon 4. Once open, activate the ArcToolbox window (if not already visible) by clicking the red box below 5. Then right‐click ArcToolbox Window (see image below) select ‘Add Toolbox.’ Then go to location of downloaded toolbox and select ‘SDMToolbox v1.0.tbx’ 6. The toolbox should appear inside the ArcToolbox (see highlighted toolbox to right). If there, now the toolbox is almost installed. 7. To finish installation simply close the ArcCatalog program. 8. Now start ArcMap and begin using the SDMtoobox! How to update or uninstall SDMtoolbox 1. Close all ArcGIS programs 2. Open ArcCatalog 10 (a program in the ESRI ArcGIS programs, see icon below) Above: ArcCatalog Icon 3. Once open, activate the ArcToolbox window (if not already visible) by clicking the red box below 4. Then right‐click SDMtoollbox in ArcToolbox Window (see Image to right) and select ‘Remove’. 5. If only uninstalling, then you are done. If installing a new version of SDMtoolbox then right‐ click ArcToolbox Window (see image below) select ‘Add Toolbox.’ Then go to location of downloaded toolbox and select ‘SDMToolbox v1.X.tbx’ 6. The toolbox should appear inside the ArcToolbox (see highlighted toolbox to right). If there, now the toolbox is almost installed. 7. To finish installation simply close the ArcCatalog program. 8. Now start ArcMap and begin using the SDMtoobox! A First Run Many things will cause the SDMtoolbox to not run that have nothing to do with the toolbox itself. Upon first use, the following steps should be performed: 1. Open ArcMap10.1 and activate the ArcToolbox window (if not already visible). Bottom image on this page is the Arctoolbox window. If not visible, click toolbox icon (see image below). 2. Ensure Spatial Analyst is Enabled in ArcMap A. Go to: Customize Extensions B. Check the box next to: Spatial Analyst (and Geostatistical Analyst if available) 3. Install all relevant ArcMap 10.1 or 10.2 Patches and Service Packs. The base release of ArcMap 10.1/2 has some serious bugs that cause many analyses to fail. The only way to fix these bugs is the install all relevant patches and service packs. A. To search for these go to: http://support.esri.com/en/downloads/patches‐ servicepacks/list?productid=160&productVersions=10.1&categoryTypes=5&categoryTypes=8 Or: http://support.esri.com/en/downloads/patches‐servicepacks B. Or use the ESRI’s ‘Patch Finder for Windows’ to identify patches, then search for suggested patches/service packs (http://downloads2.esri.com/Support/downloads/other_/PatchFinder.exe) 4. Enable ‘Tool Help’ and resize windows. Open the ‘Basic Tools Raster Tools  2a. Raster to ASCII (Folder)’ tool. Double‐Click the tool (see image to right) A. In the newly opened tool click ‘Show Help’ (red box above) B. Resize the window by dragging the two windows (depicted by red arrows) so that the final tool window is as below. Note the SDMtoolbox Icon should be fully visible. Resizing the help window to this size will ensure that all diagrams are completely visible. A note on map projections Most user reported errors have to do with map projections. As follows is a checklist of things you need to check if you have a script fail. In most cases your data should be projected, with the projection specified in the GIS file. 1. If you change or define the map projection after opening the map document. You NEED to save all projected files, then close the map document and open a new map session. The first file open in your new session needs to be one of the newly projected files—this defines the map datum. This is particularly important if you change the spatial units as the result of projection, e.g. decimal degrees to meters. If you do not do this, often SDMtoolbox scripts will fail or result in inaccurate results. 2. If the tool requires a CSV of coordinates AND your analyses are going to be in another projection, remember to convert input coordinates (or XYs) to the new, and same, datum prior to running tools or for use in species distribution modeling. For most, the quickest way to do this for CSV files (and other tables) is to: 1) Import the CSV to a shape file (Table & Shapefile Tools  CSV to shapefile tool) 2) Define input projection of shapefile and then project to the new projection (a. ArcGIS define projection and b. project tools) 3) Add the new coordinates/XYs to Shapefile using the ArcGIS Add XYs tool 4) Export shapefile table as CSV file (SDMtoolbox the Table & Shapefile Tools Shapefile to CSV tool) If using an equal‐areas projection and input data are WGS‐1984 coordinates, try the SDMtoolbox tool that will do all the uploads/Management/ user-guide-sdmtoolbox.pdf