Package: cati 0.99.5

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.

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

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cati/json (API)

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

Peer review:

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

Pkgdown:https://adrientaudiere.github.io

Datasets:

On CRAN:

5.39 score 11 stars 15 scripts 414 downloads 6 mentions 49 exports 121 dependencies

Last updated 28 days agofrom:fbf862261d. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winNOTENov 05 2024
R-4.5-linuxNOTENov 05 2024
R-4.4-winNOTENov 05 2024
R-4.4-macNOTENov 05 2024
R-4.3-winNOTENov 05 2024
R-4.3-macNOTENov 05 2024

Exports:AbToIndas.listofindexbarPartvarbarplot.decompCTREbarplot.TstatsComIndexComIndexMultiCVNNDdecompCTREFredfunky.colIndexByGroupsMinMaxMSTMinNNDMNDMNNDpartvarpiePartvarplot.ComIndexplot.ComIndexMultiplot.listofindexplot.traitflexplot.TstatsplotCorTstatsplotDistriplotRandtestplotSESvarplotSpPopplotSpVarprint.ComIndexprint.ComIndexMultiprint.traitflexprint.TstatsPvalRandComRaoRelsamplingSubsetDataSDNDSDNNDsesses.listofindexses.Tstatssum_TstatsSumBLsummary.ComIndexsummary.ComIndexMultisummary.Tstatstraitflex.anovaTstats

Dependencies:abindade4apecaretclasscliclockclustercodetoolscolorspacecpp11crayondata.tabledeldirdiagramdigestdoParalleldplyre1071fansifarverfastclusterFDFNNforeachfuturefuture.applygenericsgeometryggplot2globalsgluegowergtablehardhathexbinhitandrunhmshypervolumeinterpipredisobanditeratorsjpegkernlabKernSmoothkslabelinglatticelatticeExtralavalifecyclelinproglistenvlpSolvelubridatemagicmagrittrmapsMASSMatrixmclustmgcvModelMetricsmulticoolmunsellmvtnormnlmennetnumDerivpalmerpenguinsparallellypbapplypdistpermutepillarpixmappkgconfigplyrpngpracmaprettyunitspROCprodlimprogressprogressrproxypurrrR6rasterrasterVisrcddRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressrecipesreshape2rlangrpartscalesshapespSQUAREMstringistringrsurvivalterratibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsveganviridisLitewithrzoo

Readme and manuals

Help Manual

Help pageTopics
Internal function. Transform abundance data matrix into individual like matrix.AbToInd
Transform index results in a list of indexas.listofindex
Auxiliary functionsfunky.col
Computing metrics to test and quantify the non-random assembly of communitiesComIndex plot.ComIndex print.ComIndex summary.ComIndex
Computing multitraits metrics to test and quantify the non-random assembly of communitiesComIndexMulti plot.ComIndexMulti print.ComIndexMulti summary.ComIndexMulti
Variance partitioning for multiple traitsbarplot.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. 2008Fred
Apply metrics to groups.IndexByGroups
Ratio of the shortest distance to the longest distance in a minimum spanning treeMinMaxMST
Coefficient of variation, mean, minimum and standard deviation of the nearest neigbourhood distance.CVNND MinNND MND MNND SDND SDNND
Variance partitioning accross nested scalesbarPartvar partvar piePartvar
Plot community assembly indexplot.listofindex
Plot the bivariate relationships between T-statisticsplotCorTstats
Plot function to represent density of trait valuesplotDistri
Plot result of observed indices values against null distributionplotRandtest
Plot SES values against a variableplotSESvar
Plot populations values against species valuesplotSpPop
Plot populations values against species valuesplotSpVar
Calcul of p-value for object of class Tstats, ComIndex, ComIndexMulti and listofindexPval
Toy model to simulate internal and/or external filteringRandCom
Alpha, gamma and beta-components for taxonomic, functional and phylogenetic diversityRaoRel
Sampling subset of data.samplingSubsetData
Standardized effect size and confidence interval for a matrix of statisticsses
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 decompCTREplot.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