Package: cati 0.99.6.9000

cati: Community Assembly by Traits: Individuals and Beyond

Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models. Provides tools to analyse 'intraspecific' trait variability and its consequences for community assembly. Implements a framework using individual-level trait data to decompose variance at the population, species, and community levels. Methods are described in 'Taudiere' and 'Violle' (2016) <doi:10.1111/ecog.01433>.

Authors:Adrien Taudiere [aut, cre, cph], Cyrille Violle [aut], François Munoz [ctb]

cati_0.99.6.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cati/json (API)

# Install 'cati' in R:

install.packages('cati', repos = c('https://adrientaudiere.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adrientaudiere/cati/issues

Pkgdown/docs site:https://adrientaudiere.github.io

Datasets:

ind.plot.finch - Finch morphological data
sp.finch - Finch morphological data
traits.finch - Finch morphological data

On CRAN:

5.17 score 13 stars 19 scripts 637 downloads 6 mentions 34 exports 119 dependencies

Last updated from:9fc989cb6b. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	428
source / vignettes	OK	298
linux-release-x86_64	OK	359
macos-release-arm64	OK	234
macos-oldrel-arm64	OK	207
windows-devel	OK	347
windows-release	OK	306
windows-oldrel	OK	288
wasm-release	OK	203

Exports:AbToInd as.listofindex barPartvar ComIndex ComIndexMulti CVNND decompCTRE Fred IndexByGroups MinMaxMST MinNND MND MNND partvar piePartvar plotCorTstats plotDistri plotRandtest plotSESvar plotSpPop plotSpVar Pval RandCom RaoRel samplingSubsetData SDND SDNND ses ses.listofindex ses.Tstats sum_Tstats SumBL traitflex.anova Tstats

Dependencies:abind ade4 ape caret class cli clock cluster codetools cpp11 crayon data.table deldir diagram digest doParallel dplyr e1071 farver fastcluster FNN foreach future future.apply generics geometry ggplot2 globals glue gower gtable hardhat hexbin hitandrun hms hypervolume interp ipred isoband iterators jpeg kernlab KernSmooth ks labeling lattice latticeExtra lava lifecycle linprog listenv lpSolve lubridate magic magrittr maps MASS Matrix mclust mgcv ModelMetrics multicool mvtnorm nlme nnet numDeriv palmerpenguins parallelly pbapply pdist permute pillar pixmap pkgconfig plyr png pracma prettyunits pROC prodlim progress progressr proxy purrr R6 raster rasterVis rcdd RColorBrewer Rcpp RcppArmadillo RcppEigen RcppProgress recipes reshape2 rlang rpart S7 scales shape sp sparsevctrs SQUAREM stringi stringr survival terra tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs vegan viridisLite withr zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cati: Community Assembly by Traits: Individuals and Beyond	cati-package cati
Internal function. Transform abundance data matrix into individual like matrix.	AbToInd
Transform index results in a list of index	as.listofindex
Auxiliary functions	funky.col
Computing metrics to test and quantify the non-random assembly of communities	ComIndex plot.ComIndex print.ComIndex summary.ComIndex
Computing multitraits metrics to test and quantify the non-random assembly of communities	ComIndexMulti plot.ComIndexMulti print.ComIndexMulti summary.ComIndexMulti
Variance partitioning for multiple traits	barplot.decompCTRE decompCTRE
Finch morphological data	.Random.seed finch.ind ind.plot.finch sp.finch traits.finch
Functional richness, evenness and divergence following Villeger et al. 2008	Fred
Apply metrics to groups.	IndexByGroups
Ratio of the shortest distance to the longest distance in a minimum spanning tree	MinMaxMST
Coefficient of variation, mean, minimum and standard deviation of the nearest neigbourhood distance.	CVNND MinNND MND MNND SDND SDNND
Variance partitioning accross nested scales	barPartvar partvar piePartvar
Plot community assembly index	plot.listofindex
Plot the bivariate relationships between T-statistics	plotCorTstats
Plot function to represent density of trait values	plotDistri
Plot result of observed indices values against null distribution	plotRandtest
Plot SES values against a variable	plotSESvar
Plot populations values against species values	plotSpPop
Plot populations values against species values	plotSpVar
Calcul of p-value for object of class Tstats, ComIndex, ComIndexMulti and listofindex	Pval
Toy model to simulate internal and/or external filtering	RandCom
Alpha, gamma and beta-components for taxonomic, functional and phylogenetic diversity	RaoRel
Sampling subset of data.	samplingSubsetData
Standardized effect size and confidence interval for a matrix of statistics	ses
Standardized effect size for a list of index.	ses.listofindex
Sum of branch length of a classification dendrogram (Petchey and Gaston, 2002)	SumBL
Variance decomposition for a given trait used in decompCTRE	plot.traitflex print.traitflex traitflex.anova
Computing observed T-statistics (T for Traits) and null expectations.	barplot.Tstats plot.Tstats print.Tstats ses.Tstats summary.Tstats sum_Tstats Tstats