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]

fdcoexist_0.0.1.tar.gz
fdcoexist_0.0.1.zip(r-4.7)fdcoexist_0.0.1.zip(r-4.6)fdcoexist_0.0.1.zip(r-4.5)
fdcoexist_0.0.1.tgz(r-4.6-any)fdcoexist_0.0.1.tgz(r-4.5-any)
fdcoexist_0.0.1.tar.gz(r-4.6-any)
fdcoexist_0.0.1.tgz(r-4.5-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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/docs site:https://rekyt.github.io

On CRAN:

2.70 score 1 scripts 22 exports 31 dependencies

Last updated from:08d75af742. Checks:6 NOTE, 2 OK, 1 ERROR. Indexed: yes.

The latest version of this package failed to build. Look at thebuild logs for more information.

Target	Result	Time
linux-devel-x86_64	NOTE	314
source / vignettes	OK	327
linux-release-x86_64	NOTE	270
macos-release-arm64	NOTE	145
macos-oldrel-arm64	NOTE	122
windows-devel	NOTE	109
windows-release	NOTE	94
windows-oldrel	ERROR	86
wasm-release	OK	249

Exports:%>%alphaterm bevHoltFct check_trait_weights compute_compet_distance compute_hierarchical_compet create_trait_weights env_curve extract_growth_rates extract_mismatches generate_cor_traits generate_cor_traits_rand mismatch multigen plot_patch plot_rh r_env sp_ab_gr wtd_kurtosis wtd_mean wtd_skewness wtd_var

Dependencies:cli cpp11 dplyr farver generics ggplot2 glue gtable isoband labeling lifecycle magrittr matrixStats pillar pkgconfig purrr R6 RColorBrewer rlang S7 scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite Weighted.Desc.Stat withr

fdcoexist equation only

General Population Growth Equation | Limiting similarity ($\delta_{ij}$ & $\sigma_{ij}$) | Basic Limiting Similarity | Variable contribution of traits to limiting similarity | Considering non-linear of traits on limiting similarity | Adding intra-specific competition | Variable contribution of traits to environmental filtering | Adding Hierarchical Competition | Basic Hierarchical Competition | Variable contribution of traits to hierarchical competition | Considering non-linear effect of hierarchical competiton | Updated final equation | Considering Species Dispersal Across Patches | Final equation | Single trait contributing to everything | Multiple traits co-contributing to some processes

Rendered fromequation_only.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Function definition for deterministic model run with global dispersal Compute alpha term in Beverton-Holt function	alphaterm
Beverton-Holt function	bevHoltFct
Check trait weights data.frame	check_trait_weights
Compute trait distance between species	compute_compet_distance
Compute Hierarchical Competition coefficient at each time step	compute_hierarchical_compet
Generates a data.frame of trait weights	create_trait_weights
Species growth rate for a given trait and environment	env_curve
Extract different growth rates from fdcoexist simulation	extract_growth_rates
Extract species mismatches	extract_mismatches
Generate correlated traits	generate_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. abundance	mismatch
Function to run the simulation	multigen
Plot patch dynamics	plot_patch
Plot hierarchical growth of species in all the patches	plot_rh
Plot environmental response curves of species in all the patches	r_env
Extract Species by Patch Growth Rates and Optimal Patches	r_env_CT
Scale distance or matrix between 0 and 1	scale_distance
Plot environmental response curves of species in all the patches	sp_ab_gr
Weighted Kurtosis with na.rm	wtd_kurtosis
Weighted mean that allows NA in values and weights	wtd_mean
Weighted Skewness with na.rm	wtd_skewness
Weighted Variance	wtd_var