This is a set of small Java programs to conduct common tasks in preparing data for species distribution modeling. The programs need to be run from the command-line, using a command like java -jar nameOfProgram.jar. When run like this, the program will print out the flags that can be used to specify input files and control the program.
The applymask.jar program applies a landmask to an environmental raster. We have used this to homogenize the landmask between rasters in Bio-ORACLE. It adds no-data-values where data is available in pixels that are not supposed to have data and interpolates from surrounding pixels if a pixel that is supposed to have data doesn't have data.
The extractDataForCoordinates.jar program extracts data from a set of rasters in a folder for a file with species occurrence records (geographic coordinates). We use this to generate SWD files for Maxent runs.
The moveCoordinatesToClosestDataPixel.jar program reads a set of occurrence records. For every record that is situated in a no-data-pixel, the record is moved to the closest pixel that has data. The new coordinates are provided in csv format suitable for Maxent runs.
If you find these tools useful, please cite them in your work. I recommend citing them as follows: Verbruggen H. (2017) RasterTools: moveCoordinatesToClosestDataPixel.jar version 1.04. https://github.com/hverbruggen/RasterTools (or similar citation for the other scripts).
The RasterTools are in development and have not been tested extensively. It is quite plausible that incorrectly formatted input could lead to nonsensical output.