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cati (version 0.99.2)

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

361

Version

0.99.2

License

GPL (>= 2)

Issues

0

Pull Requests

0

Stars

12

Forks

7

Maintainer

Adrien Taudiere

Last Published

May 9th, 2018

Functions in cati (0.99.2)

plotSpVar

Plot populations values against species values
plotCorTstats

Plot the bivariate relationships between T-statistics
plotDistri

Plot function to represent density of trait values
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
plotRandtest

Plot result of observed indices values against null distribution
ses.listofindex

Standardized effect size for a list of index.
plotSESvar

Plot SES values against a variable
plotSpPop

Plot populations values against species values
ComIndexMulti

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

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

Apply metrics to groups.
MinMaxMST

Ratio of the shortest distance to the longest distance in a minimum spanning tree
cati-package

Community Assembly by Traits: Individuals and Beyond
decompCTRE

Variance partitioning for multiple traits
finch.ind

Finch morphological data
Neigbourhood distance metrics

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

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

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

Transform index results in a list of index
partvar

Variance partitioning accross nested scales
Pval

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

Auxiliary functions
AbToInd

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

Toy model to simulate internal and/or external filtering
RaoRel

Alpha, gamma and beta-components for taxonomic, functional and phylogenetic diversity
plot.listofindex

Plot community assembly index
SumBL

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