Claddis is an R package designed to import cladistic-type data sets (#NEXUS format) into R and perform disparity analysis and rate tests.
Claddis is on CRAN (version 0.6.3) but is also being developed on GitHub. To get the absolute latest version you can use:
if(!require(devtools)) install.packages("devtools", dependencies = TRUE)
devtools::install_github("graemetlloyd/Claddis", ref = "master")However, installing a development version of a package is only recommended for expert users.
Please also consult the CHANGELOG file for all updates (including new functions, features and bug fixes) to Claddis.
You can install Claddis in R via CRAN with:
install.packages("Claddis", dependencies = TRUE)Or from GitHub with:
if(!require(devtools)) install.packages("devtools", dependencies = TRUE)
devtools::install_github("graemetlloyd/Claddis", ref = "CRAN")And load it into memory using:
library(Claddis)Basic help can be found with:
?CladdisAnd clicking on the Index link at the base of the help file will reveal links to every available function.
Note that I have previously linked to tutorials for the package here, but substantial reworking of the core code means these will no longer work and so currently the example code in each function’s help file is the best substitute for this. New tutorials will eventually be produced and shared here.
Users should also be aware of the dispRity R package, that can form the end of a Claddis disparity pipeline.
The first formal paper describing Claddis was published as Lloyd (2016):
Lloyd, G. T., 2016. Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions. Biological Journal of the Linnean Society, 118, 131-151.
The effects of ancestral state estimation choices on phylomorphospaces was discussed in Lloyd (2018):
Lloyd, G. T., 2018. Journeys through discrete-character morphospace: synthesizing phylogeny, tempo, and disparity. Palaeontology, 61, 637-645.