dispRity is a R modular package for measuring disparity from multidimensional matrices.

Check out the presentation or the video of some of the package's novel features.

Installing dispRity

if(!require(devtools)) install.packages("devtools")
library(devtools)
install_github("TGuillerme/dispRity", ref = "release")
library(dispRity)

The following installs the latest release of dispRity (see patch notes below). For the piping hot development version (not recommended), replace the ref = "release" option with ref = "master". If you're using the master branch, see the patch notes for the latest developments.

Installation problems? Make sure you're using the latest R version (or at least > 4.0) and try again.

Vignettes

See the package manual online here or download the pdf version here.

Additionally, you can learn more about the structure of dispRity objects here.

Patch notes

• 2017/08/21 - v0.4.0 user friendly
  • Entirely rewritten manual (in GitBook)!
  • Removed hyper.volume metric for dependencies reasons
  • Removed parallel option from boot.matrix (the new architecture is already super fast: >2sec for 5k taxa and 10k bootstraps!)
  • New function: Claddis.ordination and geomorph.ordination for automatically ordinating data from Claddis and geomorph packages!
  • New function: char.diff for calculating character differences and associated plot function (plot.char.diff)
  • New utility function: merge.subsamples for... merging subsamples!
  • New utility function: size.subsamples for... getting the size of subsamples in a disparity object!
  • New wrapping functions: dispRity.through.time and dispRity.per.group now runs easy default disparity analysis.
  • Input ordinated matrices do not need to be of maximum size n*(n-1). Bigger matrices now only trigger a warning.
  • Changed name: series as a part of dispRity objects is now changed to subsamples throughout the whole package.
  • Changed name: time.series is now renamed time.subsamples, if dates are provided and method is discrete, this function doesn't need a phylogeny any more.
  • Changed name: get.subsamples.dispRity is now renamed get.subsamples.
  • Modified function: cust.series is now renamed custom.subsamples (to avoid confusion with custard.subsamples!). Its factor argument as been changed to groups and can now take a simple list.
  • Added dimensions optional argument to dispRity to overwrite the number of dimensions generated by boot.matrix.
  • variances, ranges and centroids are now simplified for speed. The optional arguments for data cleaning are now passed to make.metric.
  • space.maker now allows to approximate the dimensions variance distribution with the scree option.

Previous patch notes and notes for the next version can be seen here.

Authors

• Thomas Guillerme
• Natalie Cooper
• Mark Puttick

Citation

If you are using this package, please cite the following Zenodo DOI (an associated paper will be added soon):

• Guillerme, T. (2016). dispRity: a package for measuring disparity in R. Zenodo. 10.5281/zenodo.55646

BibTeX, EndNote, DataCite, RefWorks

Acknowledgments

Some ideas/functionalities/implementations in this package where implemented following the suggestions of Natalie Cooper, Graeme Lloyd, Dave Bapst, Andrew Jackson and Martin Brazeau.