virtualspecies-package {virtualspecies}

Generation of virtual species

Description

This package allows generating virtual species distributions, for example for testing species distribution modelling protocols. For a complete tutorial, see borisleroy.com/virtualspecies

Details

The process of generating a virtual species distribution is divided into four major steps.

1. Generate a virtual species distributions from environmental variables. This can be done by

   • defining partial response functions to each environmental variable, and then combining them to compute the overall environmental suitability, with generateSpFromFun

   • computing a PCA among environmental variables, and simulating the response of the species along the two first axes of the PCA with generateSpFromPCA

   This step can be randomised with generateRandomSp

2. Convert the virtual species distribution into presence-absence, with convertToPA

3. Facultatively, introduce a distribution bias with limitDistribution

4. Sample occurrence points (presence only or presence-absence) inside the virtual species distribution, either randomly or with biases, with sampleOccurrences

There are other useful functions in the package:

• formatFunctions: this is a helper function to format and illustrate the response functions as a correct input for generateSpFromFun

• plotResponse: to visualise the species-environment relationship of the virtual species

• removeCollinearity: this function can be used to remove collinearity among variables of a stack by selecting a subset of non-colinear variables

• synchroniseNA: this function can be used to synchronise NA values among layers of a stack

This packages makes use of different other packages:

• This package makes extensive use of the package terra to obtain spatialised environmental variables, and produce spatialised virtual species distributions.

• ade4 is used to generate species with a PCA approach.

• rnaturalearth is used to obtain free world shapefiles, in order to create dispersal limitations and sampling biases.

Author(s)

Boris Leroy [e-mail]

with help from C. N. Meynard, C. Bellard & F. Courchamp

Maintainer: Boris Leroy [e-mail]

References

Leroy, B. et al. 2016. virtualspecies, an R package to generate virtual species distributions. Ecography. 39(6):599-607