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>.

Version: 1.0.0
Depends: R (≥ 3.5)
Imports: optimx, stats, mvtnorm
Suggests: ggplot2, tidyr, dplyr, magrittr, knitr, stringr, rmarkdown, testthat (≥ 0.8.0), BB, ucminf, dfoptim, minqa, hydroPSO, GenSA, DEoptimR, nloptr
Published: 2021-04-16
Author: David Garcia-Callejas ORCID iD [aut, cre], Ignasi Bartomeus ORCID iD [aut], Oscar Godoy ORCID iD [aut], Maxime Lancelot [ctb]
Maintainer: David Garcia-Callejas <david.garcia.callejas at gmail.com>
BugReports: https://github.com/RadicalCommEcol/cxr/issues
License: MIT + file LICENSE
URL: https://github.com/RadicalCommEcol/cxr
NeedsCompilation: no
Citation: cxr citation info
Materials: README NEWS
CRAN checks: cxr results

Documentation:

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

Downloads:

Package source: cxr_1.0.0.tar.gz
Windows binaries: r-devel: cxr_1.0.0.zip, r-release: cxr_1.0.0.zip, r-oldrel: cxr_1.0.0.zip
macOS binaries: r-release (arm64): cxr_1.0.0.tgz, r-oldrel (arm64): cxr_1.0.0.tgz, r-release (x86_64): cxr_1.0.0.tgz, r-oldrel (x86_64): cxr_1.0.0.tgz

Linking:

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