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TITAN2 (version 2.1)

Threshold Indicator Taxa Analysis

Description

Uses indicator species scores across binary partitions of a sample set to detect congruence in taxon-specific changes of abundance and occurrence frequency along an environmental gradient as evidence of an ecological community threshold. Relevant references include: Baker, ME and RS King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1(1): 25:37. King, RS and ME Baker. 2010. Considerations for identifying and interpreting ecological community thresholds. Journal of the North American Benthological Association 29(3):998-1008. Baker ME and RS King. 2013. Of TITAN and straw men: an appeal for greater understanding of community data. Freshwater Science 32(2):489-506.

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Version

Install

install.packages('TITAN2')

Monthly Downloads

307

Version

2.1

License

GPL-2

Maintainer

David Kahle

Last Published

December 19th, 2015

Functions in TITAN2 (2.1)

boot.titan

Controls the allocation of bootstrap replicates
glades.taxa

glades.taxa title
obs.summ

Summarizes results from TITAN's analaysis of observed data
plotTaxa

Plots taxon-specific change points
getivz

Performs calculation of IndVal z scores from observed and permuted values
indvalp

Calculate permuted IndVal scores using a group matrix
glades.env

glades.env title
ivzsums

Sum IndVal z scores across taxa
glades.titan

glades.titan title
txa.screen

Screening of site by taxa matrix
sumz.tab

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

Summarizes raw output from TITAN's bootstrap procedure
tboot

Calculate bootstrapped IndVal z scores
permiv

Permutation of group membership for a single candidate partition
indval

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

The primary function call for package TITAN
env.part

Partitions environmental gradient for analysis
plotCPs

Plots probability densities of empirical distributions of bootstrapped change points
TITAN2

Threshold Indicator Taxa Analysis
plotSumz

Plots the pattern of community change along an environmental gradient