R: Community Assembly by Traits: Individuals and Beyond

# Community Assembly by Traits: Individuals and Beyond

## Documentation for package ‘cati’ version 0.99.6

- DESCRIPTION file.
- Package NEWS.

## Help Pages

cati-package | cati: Community Assembly by Traits: Individuals and Beyond
.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.
cati | cati: Community Assembly by Traits: Individuals and Beyond
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.