Package index

All functions

AbToInd()

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

funky.col()

Auxiliary functions

CVNND() MNND() MinNND() SDNND() SDND() MND()

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

ComIndex() plot(<ComIndex>) print(<ComIndex>) summary(<ComIndex>)

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

ComIndexMulti() plot(<ComIndexMulti>) print(<ComIndexMulti>) summary(<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

Pval()

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

RandCom()

Toy model to simulate internal and/or external filtering

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)

Tstats() sum_Tstats() ses.Tstats() barplot(<Tstats>) plot(<Tstats>) print(<Tstats>) summary(<Tstats>)

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

as.listofindex()

Transform index results in a list of index

decompCTRE() barplot(<decompCTRE>)

Variance partitioning for multiple traits

finch.ind

Finch morphological data

partvar() barPartvar() piePartvar()

Variance partitioning accross nested scales

plot(<listofindex>)

Plot community assembly index

plotCorTstats()

Plot the bivariate relationships between T-statistics

plotDistri()

Plot function to represent density of trait values

plotRandtest()

Plot result of observed indices values against null distribution

plotSESvar()

Plot SES values against a variable

plotSpPop()

Plot populations values against species values

plotSpVar()

Plot populations values against species values

samplingSubsetData()

Sampling subset of data.

ses()

Standardized effect size and confidence interval for a matrix of statistics

ses.listofindex()

Standardized effect size for a list of index.

traitflex.anova() plot(<traitflex>) print(<traitflex>)

Variance decomposition for a given trait used in decompCTRE