README.md

In Farewe/virtualspecies: Generation of Virtual Species Distributions

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virtualspecies

The virtualspecies R package

This package provides a user-friendly framework for generating virtual species distribution, integrating the existing methodological approaches. The package includes (1) generating virtual species’ suitability from a spatial set of environmental conditions, with two different approaches; (2) converting the environmental suitability into presence-absence with a probabilistic approach; (3) introducing dispersal limitations in the realised virtual species distributions and (4) sampling occurrences with different biases in the sampling procedure.

There is a full online tutorial available here: http://borisleroy.com/virtualspecies/

Update 1.6 : shift from raster to terra

virtualspecies has been updated to version 1.6 in September 2023. The major change in this update is that now this package relies upon the R package terra rather than raster; in addition, internally it uses functions from the package sf rather than sp. This update was required since multiple spatial packages are going to be retired from R, and future developments and improvements of spatial packages will rely on terra and sf.

This update may cause some breaking changes. I maintained the changes as minimal as possible so that previous code (version <= 1.5) will still be compatible with the new code (version >= 1.6). However, objects generated in versions <= 1.5 will likely not be compatible with the package version 1.6. They can still be converted manually to become compatible, using functions from the package terra such as rast(). If you find yourself in trouble, email me about that. In addition, the methods in functions limitDistribution() and sampleOccurrences() have changed slightly because they now use the package rnaturaleath (formerly they used rworldmap).

Farewe/virtualspecies documentation built on Jan. 31, 2024, 6:12 a.m.