Community Assembly by Traits: Individuals and Beyond


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Documentation for package ‘cati’ version 0.99.3

Help Pages

.Random.seed Finch morphological data
AbToInd Internal function. Transform abundance data matrix into individual like matrix.
as.listofindex Transform index results in a list of index
barPartvar Variance partitioning accross nested scales
barplot.decompCTRE Variance partitioning for multiple traits
barplot.Tstats Computing observed T-statistics (T for Traits) and null expectations.
ComIndex Computing metrics to test and quantify the non-random assembly of communities
ComIndexMulti Computing multitraits metrics to test and quantify the non-random assembly of communities
CVNND Coefficient of variation, mean, minimum and standard deviation of the nearest neigbourhood distance.
decompCTRE Variance partitioning for multiple traits
finch.ind Finch morphological data
Fred Functional richness, evenness and divergence following Villeger et al. 2008
funky.col Auxiliary functions
ind.plot.finch Finch morphological data
IndexByGroups Apply metrics to groups.
MinMaxMST Ratio of the shortest distance to the longest distance in a minimum spanning tree
MinNND Coefficient of variation, mean, minimum and standard deviation of the nearest neigbourhood distance.
MND Coefficient of variation, mean, minimum and standard deviation of the nearest neigbourhood distance.
MNND Coefficient of variation, mean, minimum and standard deviation of the nearest neigbourhood distance.
partvar Variance partitioning accross nested scales
piePartvar Variance partitioning accross nested scales
plot.ComIndex Computing metrics to test and quantify the non-random assembly of communities
plot.ComIndexMulti Computing multitraits metrics to test and quantify the non-random assembly of communities
plot.listofindex Plot community assembly index
plot.traitflex Variance decomposition for a given trait used in decompCTRE
plot.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
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
print.ComIndex Computing metrics to test and quantify the non-random assembly of communities
print.ComIndexMulti Computing multitraits metrics to test and quantify the non-random assembly of communities
print.traitflex Variance decomposition for a given trait used in decompCTRE
print.Tstats Computing observed T-statistics (T for Traits) and null expectations.
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
samplingSubsetData Sampling subset of data.
SDND Coefficient of variation, mean, minimum and standard deviation of the nearest neigbourhood distance.
SDNND Coefficient of variation, mean, minimum and standard deviation of the nearest neigbourhood distance.
ses Standardized effect size and confidence interval for a matrix of statistics
ses.listofindex Standardized effect size for a list of index.
ses.Tstats Computing observed T-statistics (T for Traits) and null expectations.
sp.finch Finch morphological data
SumBL Sum of branch length of a classification dendrogram (Petchey and Gaston, 2002)
summary.ComIndex Computing metrics to test and quantify the non-random assembly of communities
summary.ComIndexMulti Computing multitraits metrics to test and quantify the non-random assembly of communities
summary.Tstats Computing observed T-statistics (T for Traits) and null expectations.
sum_Tstats Computing observed T-statistics (T for Traits) and null expectations.
traitflex.anova Variance decomposition for a given trait used in decompCTRE
traits.finch Finch morphological data
Tstats Computing observed T-statistics (T for Traits) and null expectations.