# Threshold Indicator Taxa Analysis

## Documentation for package ‘TITAN2’ version 2.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

big.boot | Summarizes raw output from TITAN's bootstrap procedure
boot.titan | Controls the allocation of bootstrap replicates
env.part | Partitions environmental gradient for analysis
getivz | Performs calculation of IndVal z scores from observed and permuted values
glades.env | glades.env title
glades.taxa | glades.taxa title
glades.titan | glades.titan title
indval | IndVal scores based on relative abundance across, and occurrence frequency within, groups
indvalp | Calculate permuted IndVal scores using a group matrix
indvalps | Calculate permuted IndVal scores using a group matrix
indvals | IndVal scores based on relative abundance across, and occurrence frequency within, groups
ivzsums | Sum IndVal z scores across taxa
ivzsums.f | Sum IndVal z scores across taxa
obs.summ | Summarizes results from TITAN's analaysis of observed data
package-TITAN2 | Threshold Indicator Taxa Analysis
permiv | Permutation of group membership for a single candidate partition
plot-cps | Plots probability densities of empirical distributions of bootstrapped change points
plot-sumz | Plots the pattern of community change along an environmental gradient
plot-taxa | Plots taxon-specific change points
plotCPs | Plots probability densities of empirical distributions of bootstrapped change points
plotSumz | Plots the pattern of community change along an environmental gradient
plotTaxa | Plots taxon-specific change points
plot_cps | Plots probability densities of empirical distributions of bootstrapped change points
plot_sumz | Plots the pattern of community change along an environmental gradient
plot_sumz_density | Plot community level change
plot_taxa | Plots taxon-specific change points
plot_taxa_ridges | Taxon change point ridge plots
small.boot | Summarizes raw output from TITAN's bootstrap procedure
smallBigBoot | Summarizes raw output from TITAN's bootstrap procedure
sumz.tab | Summarizes the results of the community-level sum(z) analysis
tboot | Calculate bootstrapped IndVal z scores
titan | Perform a threshold indicator taxa analysis
TITAN2 | Threshold Indicator Taxa Analysis
txa.screen | Screening of site by taxa matrix