TITAN2: Threshold Indicator Taxa Analysis

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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.

Author
Matthew E. Baker [aut, cph], Ryan S. King [aut, cph], David Kahle [aut, cph, cre]
Date of publication
2015-12-19 18:49:09
Maintainer
David Kahle <david.kahle@gmail.com>
License
GPL-2
Version
2.1

View on CRAN

Man pages

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...
glades.env
glades.env title
glades.taxa
glades.taxa title
glades.titan
glades.titan title
indval
IndVal scores based on relative abundance across, and...
indvalp
Calculate permuted IndVal scores using a group matrix
ivzsums
Sum IndVal z scores across taxa
obs.summ
Summarizes results from TITAN's analaysis of observed data
permiv
Permutation of group membership for a single candidate...
plotCPs
Plots probability densities of empirical distributions of...
plotSumz
Plots the pattern of community change along an environmental...
plotTaxa
Plots taxon-specific change points
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
The primary function call for package TITAN
TITAN2
Threshold Indicator Taxa Analysis
txa.screen
Screening of site by taxa matrix

Files in this package

TITAN2
TITAN2/inst
TITAN2/inst/doc
TITAN2/inst/doc/glades.TITAN.R
TITAN2/inst/doc/glades.TITAN.html
TITAN2/inst/doc/glades.TITAN.Rmd
TITAN2/NAMESPACE
TITAN2/NEWS
TITAN2/data
TITAN2/data/glades.env.rda
TITAN2/data/glades.titan.rda
TITAN2/data/glades.taxa.rda
TITAN2/data/datalist
TITAN2/R
TITAN2/R/titan.R
TITAN2/R/boot.functions.R
TITAN2/R/plotCPs.R
TITAN2/R/plotSumz.R
TITAN2/R/data.R
TITAN2/R/control.functions.R
TITAN2/R/plotTaxa.R
TITAN2/R/core.functions.R
TITAN2/R/TITAN2.R
TITAN2/vignettes
TITAN2/vignettes/glades.TITAN.Rmd
TITAN2/MD5
TITAN2/build
TITAN2/build/vignette.rds
TITAN2/DESCRIPTION
TITAN2/man
TITAN2/man/getivz.Rd
TITAN2/man/indvalp.Rd
TITAN2/man/plotSumz.Rd
TITAN2/man/smallBigBoot.Rd
TITAN2/man/plotCPs.Rd
TITAN2/man/env.part.Rd
TITAN2/man/glades.titan.Rd
TITAN2/man/indval.Rd
TITAN2/man/boot.titan.Rd
TITAN2/man/glades.env.Rd
TITAN2/man/sumz.tab.Rd
TITAN2/man/titan.Rd
TITAN2/man/TITAN2.Rd
TITAN2/man/permiv.Rd
TITAN2/man/glades.taxa.Rd
TITAN2/man/obs.summ.Rd
TITAN2/man/txa.screen.Rd
TITAN2/man/plotTaxa.Rd
TITAN2/man/tboot.Rd
TITAN2/man/ivzsums.Rd