cxr: A Toolbox for Modelling Species Coexistence in R

Recent developments in modern coexistence theory have advanced our understanding on how species are able to persist and co-occur with other species at varying abundances. However, applying this mathematical framework to empirical data is still challenging, precluding a larger adoption of the theoretical tools developed by empiricists. This package provides a complete toolbox for modelling interaction effects between species, and calculate fitness and niche differences. The functions are flexible, may accept covariates, and different fitting algorithms can be used. A full description of the underlying methods is available in García-Callejas, D., Godoy, O., and Bartomeus, I. (2020) <doi:10.1111/2041-210X.13443>. Furthermore, the package provides a series of functions to calculate dynamics for stage-structured populations across sites.

Version: 1.1.1
Depends: R (≥ 3.5)
Imports: Matrix, mvtnorm, optimx, stats
Suggests: BB, DEoptimR, dfoptim, dplyr, GenSA, ggplot2, knitr, magrittr, minqa, nloptr, rmarkdown, stringr, testthat (≥ 0.8.0), tidyr, ucminf
Published: 2023-10-26
DOI: 10.32614/CRAN.package.cxr
Author: David Garcia-Callejas ORCID iD [aut, cre], Ignasi Bartomeus ORCID iD [aut], Oscar Godoy ORCID iD [aut], Maxime Lancelot [ctb], Maria Paniw [ctb]
Maintainer: David Garcia-Callejas <david.garcia.callejas at>
License: MIT + file LICENSE
NeedsCompilation: no
Citation: cxr citation info
Materials: README NEWS
CRAN checks: cxr results


Reference manual: cxr.pdf
Vignettes: Getting started
Data and model formats
coexistence metrics
User-defined Models
Abundance projections
Metapopulation projections


Package source: cxr_1.1.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): cxr_1.1.1.tgz, r-oldrel (arm64): cxr_1.1.1.tgz, r-release (x86_64): cxr_1.1.1.tgz, r-oldrel (x86_64): cxr_1.1.1.tgz
Old sources: cxr archive


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