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Published August 21, 2017 | Version v0.4
Software Open

TGuillerme/dispRity: v0.4

Creators

  • 1. Imperial College London
  • 2. Natural History Museum

Description

  • 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.

Files

TGuillerme/dispRity-v0.4.zip

Files (9.3 MB)

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Additional details

Related works

Is supplement to
https://github.com/TGuillerme/dispRity/tree/v0.4 (URL)