QSDM

QSDM – Species Distribution Modelling for the QGIS Processing Toolbox

My second plugin contribution to QGIS is called QSDM (for QGIS Species Distribution Modelling). Not a too fancy name, but it serves it purpose. I began coding it some time ago in order to run MAXENT models within QGIS and without calling any external program or script. This eases up at least for me a lot of work. The biggest problem with the MAXENT software is that it requires equal extents and shapes of all input environmental vectors. So you have to unify your environmental predictors before running the tool. I am currently in the process of writing my own much faster version of a raster unification script, but until then the excellent scripting solution from Yury aka ssrebelious works just fine. So you can just load in your layers and QSDM will reproject them to latitude-longitude (WGS-84) if necessary, unify them to a common extent if necessary and finally saves them as ESRI .asc file.

Very (!) simple prediction of Lycaena phlaeas occurence in Skane, Sweden. Only Elevation and LandCover were used as Environmental Layers in MAXENT

QSDM is designed to show and be able to run only those functions for which you have the necessary dependencies. I know that this might kick out some users, but I am not really fond of helping people installing third-party libraries. Look on the authors homepage or on the net. I am thinking of integrating more models and tools in the future, such as Logistic Regressions, Random Forest Predictions and so on. Depends a lot on my available time, personal interest and willingness.

 

What it can do (05.05.2014):

• Data Analysis
  • Calculate Niche Overlap Statistics
  • Range Shifts
• Data Preperation
  • Create Species Richness Grids
  • Data Transformation (simple)
  • Raster Unification, for now using the excellent script from Yury Ryabov
• Species Distribution Modelling
  • MAXENT (Parameter Preperation)
  • Maximum Entropy Modelling (semi-automatic modelling)
  • Maximum Entropy Modelling (Manual Configuration of parameters)

How-To-Run:

1. Make sure you have JAVA installed and it is executable. You can try it out by opening a console on your system and enter “java -version”. No error should pop up.
2. Some of the functions won’t show up in Processing until you have the necessary libraries installed. If you have enabled numpy and scipy you are on a good way. Please don’t ask me how to install libraries on your system.
3. Download the QSDM Plugin and external dependencies if you haven’t already. For MAXENT for instance you need the maxent.jar file.
4. Go to the Processing options and enable it. Make sure to set all the correct paths and folders. MAXENT normally requires a output and environmental folders. The plugins workaround is to set these folders in the Processing options.
5. Try and run some of the functions in the Processing Toolbox.
6. If unexpected Errors pop up, please try and format your layers to appropriate formats before posting hundreds of data-specific error messages, that are hard to impossible to debug remotely.

Note: This plugin is still experimental, so please don’t expect it to run without issues for all of you.