Package: TITAN2 2.4.4

TITAN2: 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 and King (2010) <doi:10.1111/j.2041-210X.2009.00007.x>, King and Baker (2010) <doi:10.1899/09-144.1>, and Baker and King (2013) <doi:10.1899/12-142.1>.

Authors:Matthew E. Baker [aut, cph], Ryan S. King [aut, cph], David Kahle [aut, cph, cre]

TITAN2_2.4.4.tar.gz
TITAN2_2.4.4.zip(r-4.7)TITAN2_2.4.4.zip(r-4.6)TITAN2_2.4.4.zip(r-4.5)
TITAN2_2.4.4.tgz(r-4.6-any)TITAN2_2.4.4.tgz(r-4.5-any)
TITAN2_2.4.4.tar.gz(r-4.7-any)TITAN2_2.4.4.tar.gz(r-4.6-any)
TITAN2_2.4.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TITAN2/json (API)

# Install 'TITAN2' in R:

install.packages('TITAN2', repos = c('https://dkahle.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dkahle/titan2/issues

Datasets:

glades.env - Glades.env title
glades.taxa - Glades.taxa title
glades.titan - Glades.titan title

On CRAN:

6.80 score 16 stars 39 scripts 412 downloads 10 mentions 10 exports 28 dependencies

Last updated from:0d6c89eda0. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	171
source / vignettes	OK	193
linux-release-x86_64	OK	141
macos-release-arm64	OK	124
macos-oldrel-arm64	OK	88
windows-devel	OK	113
windows-release	OK	141
windows-oldrel	OK	105
wasm-release	OK	110

Exports:getivz plot_cps plot_sumz plot_sumz_density plot_taxa plot_taxa_ridges plotCPs plotSumz plotTaxa titan

Dependencies:cli cowplot cpp11 dplyr farver generics ggplot2 ggridges glue gtable isoband labeling lifecycle magrittr pillar pkgconfig purrr R6 RColorBrewer rlang S7 scales tibble tidyselect utf8 vctrs viridisLite withr

An Introduction to TITAN2

Rendered fromtitan2-intro.Rmdusingknitr::rmarkdown

Last update: 2023-11-14
Started: 2019-04-04

Citation

Development and contributors

Readme and manuals

Help Manual

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