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cati (version 0.99.4)

Community Assembly by Traits: Individuals and Beyond

Description

Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models.

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Install

install.packages('cati')

Monthly Downloads

443

Version

0.99.4

License

GPL (>= 2)

Issues

0

Pull Requests

0

Stars

11

Forks

7

Maintainer

Adrien Taudiere

Last Published

February 25th, 2022

Functions in cati (0.99.4)

Pval

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

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

Auxiliary functions
RandCom

Toy model to simulate internal and/or external filtering
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.
AbToInd

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

Apply metrics to groups.
Fred

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

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

Variance partitioning for multiple traits
ses

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

Sampling subset of data.
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)
as.listofindex

Transform index results in a list of index
plotSpVar

Plot populations values against species values
plotSpPop

Plot populations values against species values
Tstats

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

Plot the bivariate relationships between T-statistics
plotDistri

Plot function to represent density of trait values
ses.listofindex

Standardized effect size for a list of index.
finch.ind

Finch morphological data
traitflex.anova

Variance decomposition for a given trait used in decompCTRE
plot.listofindex

Plot community assembly index
plotSESvar

Plot SES values against a variable
plotRandtest

Plot result of observed indices values against null distribution
partvar

Variance partitioning accross nested scales