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cati (version 0.99.3)

Community Assembly by Traits: Individuals and Beyond

Description

Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics (Violle et al. (2012) ) and other metrics, and dedicated null models described in Taudiere & Violle (2016) .

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Install

install.packages('cati')

Monthly Downloads

443

Version

0.99.3

License

GPL (>= 2)

Issues

0

Pull Requests

0

Stars

11

Forks

7

Maintainer

Adrien Taudiere

Last Published

March 2nd, 2020

Functions in cati (0.99.3)

MinMaxMST

Ratio of the shortest distance to the longest distance in a minimum spanning tree
IndexByGroups

Apply metrics to groups.
Fred

Functional richness, evenness and divergence following Villeger et al. 2008
ComIndexMulti

Computing multitraits metrics to test and quantify the non-random assembly of communities
RaoRel

Alpha, gamma and beta-components for taxonomic, functional and phylogenetic diversity
SumBL

Sum of branch length of a classification dendrogram (Petchey and Gaston, 2002)
Auxiliary functions

Auxiliary functions
plotRandtest

Plot result of observed indices values against null distribution
plotSESvar

Plot SES values against a variable
plotCorTstats

Plot the bivariate relationships between T-statistics
AbToInd

Internal function. Transform abundance data matrix into individual like matrix.
plotDistri

Plot function to represent density of trait values
partvar

Variance partitioning accross nested scales
decompCTRE

Variance partitioning for multiple traits
plotSpPop

Plot populations values against species values
finch.ind

Finch morphological data
plot.listofindex

Plot community assembly index
ses.listofindex

Standardized effect size for a list of index.
as.listofindex

Transform index results in a list of index
samplingSubsetData

Sampling subset of data.
traitflex.anova

Variance decomposition for a given trait used in decompCTRE
ses

Standardized effect size and confidence interval for a matrix of statistics
Tstats

Computing observed T-statistics (T for Traits) and null expectations.
plotSpVar

Plot populations values against species values
ComIndex

Computing metrics to test and quantify the non-random assembly of communities
Neigbourhood distance metrics

Coefficient of variation, mean, minimum and standard deviation of the nearest neigbourhood distance.
Pval

Calcul of p-value for object of class Tstats, ComIndex, ComIndexMulti and listofindex
RandCom

Toy model to simulate internal and/or external filtering