Current Status

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cxr 1.0.0

cxr provides a complete toolbox for modelling interactions between species, calculate coexistence metrics (e.g. niche and fitness differences), and project species abundances. The functions are flexible and can include covariates, use different optimization algorithms, or accept user-defined mathematical population models as starting points.


The development version can be installed via the remotes package:


Setup requirements and use

The best way to start is to follow our vignettes. Note that for installing the vignettes alongside the package, you need to use following options at install:

                         build_opts = c("--no-resave-data", "--no-manual"), 
                         build_vignettes = TRUE)

Key features

The package has several key functions:

And a set of internal functions, data and models. The functions with prefix cxr estimate model parameters from observational data, and functions without prefix calculate metrics related to species coexistence from model parameters. This basic workflow of the package is explained in different vignettes:

Once the package is installed, vignettes can be accessed in the standard way:

vignette("V1_Getting_started",package = "cxr")
vignette("V2_Data_formats",package = "cxr")
vignette("V3_Coexistence_metrics",package = "cxr")
vignette("V4_Models",package = "cxr")
vignette("V5_Abundance_projections",package = "cxr")

Citation information

When citing, please refer to both the package citation and the release paper GarcĂ­a-Callejas, Godoy, and Bartomeus, 2020.

Future developments

cxr is in continuous development. This is a partial list of features we aim to implement in future releases:

Bug reports and contributions.

We welcome contributions (e.g. via pull request) and bug reports.

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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cxr documentation built on April 16, 2021, 5:07 p.m.