TITAN2 v2.4

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Threshold Indicator Taxa Analysis

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.

Readme

TITAN2

CRAN
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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).

Functions in TITAN2

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

Name
titan2-intro.Rmd
titan2-intro.html
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Details

Type Package
VignetteBuilder knitr
License GPL-2
LazyData TRUE
RoxygenNote 7.0.2
Encoding UTF-8
NeedsCompilation no
Packaged 2019-12-05 03:57:21 UTC; david_kahle
Repository CRAN
Date/Publication 2019-12-05 09:00:05 UTC

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