Package: fdcoexist 0.0.1

fdcoexist: Multi-Species Trait-Based Coexistence Model in Discrete time

A modified Beverton-Holt model used in the Denelle, Grenié et al. manuscript that expresses environmental filtering, limiting similarity and hierarchical competition explicitely in function of species traits. This package provides all the code necessary to rerun the analyses of the manuscript.

Authors:Matthias Grenié [aut, cre], Pierre Denelle [aut], Caroline Tucker [aut], François Munoz [aut], Cyrille Violle [aut]

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fdcoexist.pdf |fdcoexist.html✨
fdcoexist/json (API)

# Install 'fdcoexist' in R:
install.packages('fdcoexist', repos = c('https://rekyt.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rekyt/fdcoexist/issues

Pkgdown site:https://rekyt.github.io

On CRAN:

Conda:

2.70 score 1 scripts 22 exports 38 dependencies

Last updated 2 years agofrom:08d75af742. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 13 2025
R-4.5-winNOTEFeb 13 2025
R-4.5-macNOTEFeb 13 2025
R-4.5-linuxNOTEFeb 13 2025
R-4.4-winNOTEFeb 13 2025
R-4.4-macNOTEFeb 13 2025
R-4.3-winNOTEFeb 13 2025
R-4.3-macNOTEFeb 13 2025

Exports:%>%alphatermbevHoltFctcheck_trait_weightscompute_compet_distancecompute_hierarchical_competcreate_trait_weightsenv_curveextract_growth_ratesextract_mismatchesgenerate_cor_traitsgenerate_cor_traits_randmismatchmultigenplot_patchplot_rhr_envsp_ab_grwtd_kurtosiswtd_meanwtd_skewnesswtd_var

Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLiteWeighted.Desc.Statwithr

fdcoexist equation only

Pierre Denelle, Matthias Grenié, Cyrille Violle, François Munoz and Caroline M. Tucker

Rendered fromequation_only.Rmdusingknitr::rmarkdownon Feb 13 2025.

Last update: 2022-10-11
Started: 2021-02-23

Readme and manuals

Help Manual

Help pageTopics
Function definition for deterministic model run with global dispersal Compute alpha term in Beverton-Holt functionalphaterm
Beverton-Holt functionbevHoltFct
Check trait weights data.framecheck_trait_weights
Compute trait distance between speciescompute_compet_distance
Compute Hierarchical Competition coefficient at each time stepcompute_hierarchical_compet
Generates a data.frame of trait weightscreate_trait_weights
Species growth rate for a given trait and environmentenv_curve
Extract different growth rates from fdcoexist simulationextract_growth_rates
Extract species mismatchesextract_mismatches
Generate correlated traitsgenerate_cor_traits
Generate random traits Compared to generate_cor_traits() introduce a little of variability in first trait as instead of being directly determined by the species number it adds little white noise to it and scale it to a minimum of 0 if negative and maximum of 25 if maximum value is over 25.generate_cor_traits_rand
Plot mismatch per species between environmental optimum and max. abundancemismatch
Function to run the simulationmultigen
Plot patch dynamicsplot_patch
Plot hierarchical growth of species in all the patchesplot_rh
Plot environmental response curves of species in all the patchesr_env
Extract Species by Patch Growth Rates and Optimal Patchesr_env_CT
Scale distance or matrix between 0 and 1scale_distance
Plot environmental response curves of species in all the patchessp_ab_gr
Weighted Kurtosis with na.rmwtd_kurtosis
Weighted mean that allows NA in values and weightswtd_mean
Weighted Skewness with na.rmwtd_skewness
Weighted Variancewtd_var