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TITAN2

TITAN2 is the second R implementation of Threshold Indicator Taxa ANalysis. It is an R package source controlled with Git on GitHub and distributed on CRAN.

To learn more about TITAN2, check out the vignette here (you can click Download to view it in a separate window).

Note: a previous version of this readme stated that you could read the vignette; however, the vignette is not built when the package is downloaded from GitHub, so just access it as above.

Installation

You can install TITAN2 in either of two ways. At the present time, we recommend installing TITAN2 from GitHub, as it has several new features, e.g. plot_taxa_ridges().

  • From Github (dev version):
if (!requireNamespace("devtools")) install.packages("devtools")
devtools::install_github("dkahle/TITAN2")
  • From CRAN:
install.packages("TITAN2")

Acknowledgements

This work continues to be supported by the Department of Geography and Environmental Systems (UMBC), Department of Biology (Baylor), and Department of Statistical Science (Baylor).

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Version

Install

install.packages('TITAN2')

Monthly Downloads

413

Version

2.4.3

License

GPL-2

Maintainer

David Kahle

Last Published

November 14th, 2023

Functions in TITAN2 (2.4.3)

permiv

Permutation of group membership for a single candidate partition
plot-sumz

Plots the pattern of community change along an environmental gradient
txa.screen

Screening of site by taxa matrix
titan

Perform a threshold indicator taxa analysis
plot_sumz_density

Plot community level change
plot_taxa_ridges

Taxon change point ridge plots
smallBigBoot

Summarizes raw output from TITAN's bootstrap procedure
tboot

Calculate bootstrapped IndVal z scores
sumz.tab

Summarizes the results of the community-level sum(z) analysis
indvalp

Calculate permuted IndVal scores using a group matrix
glades.env

glades.env title
TITAN2

Threshold Indicator Taxa Analysis
glades.titan

glades.titan title
glades.taxa

glades.taxa title
ivzsums

Sum IndVal z scores across taxa
env.part

Partitions environmental gradient for analysis
boot.titan

Controls the allocation of bootstrap replicates
indval

IndVal scores based on relative abundance across, and occurrence frequency within, groups
getivz

Performs calculation of IndVal z scores from observed and permuted values
obs.summ

Summarizes results from TITAN's analaysis of observed data
plot-cps

Plots probability densities of empirical distributions of bootstrapped change points
plot-taxa

Plots taxon-specific change points