rsdm is a package designed to help streamlining species distribution
analyses for large-scale assessments of biodiversity patterns. The
package contains a set of helper functions to facilitate the collation
and curation of species occurrence data, the building and assessment of
species distribution models, the projection and the mapping of the
geographic range of species and biodiversity patterns. It is also
equipped with experimental wrapper functions for developing modelling
pipelines and thus processing large quantities of data simultaneously.
The functions in this package were used to model the distribution of 36,687 plant species in The global distribution of plants used by humans (Pironon and Ondo et al. 2024).
Make sure to have R or Rstudio installed on your machine. Some R packages need to be compiled from source, so if you are on Windows, you need to install Rtools too.
Install rsdm with the following instructions. If the package
devtools is not already installed run install.packages("devtools")
in your console. Setting R_REMOTES_NO_ERRORS_FROM_WARNINGS="false will
cause warning messages during calls to devtools::install_github to
become errors. So beforehand, make sure to set this environmental
variable to true via:
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")Then, install and load the package:
devtools::install_github("IanOndo/rsdm")
library(rsdm)- Data gathering and (pre-)processing
- Cleaning species occurrence record (in progress)
- Modelling species distribution
Pironon and Ondo, M. Diazgranados, R. Allkin, A. C. Baquero, R. Cámara-Leret, C. Canteiro, Z. Dennehy-Carr, et al. 2024. “The Global Distribution of Plants Used by Humans.” Science 383 (6680): 293–97. https://doi.org/10.1126/science.adg8028.