Claddis is an in-development R package designed to import cladistic-type data sets (#NEXUS format) into R and perform disparity and rate tests.
Below are links to slides from three conference presentations on the package. (Note: the package has changed a lot since the first two were given!)
You can install and load Claddis into R using the following:
# Install the devtools package from CRAN:
install.packages("devtools")
# Install the phytools and Claddis packages from github:
devtools::install_github("liamrevell/phytools")
devtools::install_github("graemetlloyd/Claddis")
# Load the Claddis package into R:
library(Claddis)A brief tutorial for the package is also available here.
More will be added here in future to show the basic features of the package.
Claddis is now on CRAN, but the current version (0.1) is broken due to changes in a dependent package (phytools). Users are advised to install directly from github (version 0.2) using the code above. The first formal paper describing Claddis is now published in Biological Journal of the Linnean Society and can be cited as:
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.