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Patch notes

  • 2017/09/25 - v0.4.1
    • New function: get.bin.ages for getting the geological timescale of a tree (based on geoscale).
    • Fixed fuzzy match issues in slice.tree
  • 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.
  • 2017/01/25 - v0.3.0 dispRity lite
    • Complete change of the dispRity object architecture (see more here).
    • dispRity object utilities are now all grouped under the ?dispRity.utilities manual with appropriate S3 methods.
    • Removed rm.last.axis argument in boot.matrix. It is now replaced by dimensions.
    • Changed argument in plot.dispRity, type = "lines" is now replaced by type = "line".
    • sim.morpho can now use model = "mixed" for using both HKY-binary and Mk in characters simulation.
  • 2016/11/07 - v0.2.1 - making stuff up
    • New utility function: merge.time.series for cleaning or merging time series
    • New vignette: dispRity-simulate_data on how to simulate morphological characters in dispRity
    • New function: sim.morpho generates morphological matrices
    • New function: check.morpho for checking how "realistic" the simulate morphological matrices are
    • New utility functions: get.contrast.matrix and apply.inapplicable functions for morphological matrices
    • Minor graphical functions updates
  • 2016/06/15 - v0.2.0
    • New utility functions: pair.plot, scale.dispRity and sort.dispRity.
    • New function: space.maker for creating some multidimensional spaces!
    • New disparity metrics: convhull.surface, convhull.volume and hyper.volume
    • New disparity test null.test.
    • New plot.dispRity arguments: density for controlling the polygons density and add for adding plots.
    • Removed type_discrete argument in plot.dispRity and type argument can now be:
      • continuous disparity curves.
      • box for real boxplots.
      • lines for the distribution verticale lines.
      • polygon for the distribution boxes.
    • Minor functions corrections for specific optional arguments combinations.
    • Many updates to the functions manual and vignettes.
    • Some algorithm are now improved for speed
    • Disparity can now be calculated as a distribution (i.e. dispRity, test.dispRity, plot.dispRity, and summary.dispRity can now intake one or more distribution rather than just one or more single values of disparity; whether the data is bootstrapped or not).
    • dispRity can now intake dispRity objects with level 2 disparity metrics.
    • boot.matrix and dispRity can now run in parallel.
    • centroids disparity metric can now intake a centroid argument for fixing the centroid point value.
    • variances and ranges disparity metrics can now intake a k.root argument for scaling the results.
  • 2015/12/01 - v0.1.2
    • New function: get.dispRity for subsampling dispRity objects
    • New function: extract.dispRity for extracting disparity results
    • New function: test.dispRity for applying tests to dispRity objects
    • New function: make.metric for helping creating your very own disparity metric
    • New metric: hyper.volume for measuring the morphospace hyper-ellipsoid volume
    • metric argument from dispRity can now intake up two three functions (see dispRity.metric and make.metric)
    • Many improved functions manuals and examples!
    • Improved vignettes:
      • dispRity palaeo demo a quick demo aimed more for palaeobiologist
      • dispRity ecology demo a quick demo aimed more for ecologists
      • dispRity manual for people that want to know the package in details
      • dispRity metrics for explaining how the disparity metric implementation works
  • 2015/10/08 - v0.1.1
    • Fixed many error/warning messages
    • plot.dispRity options improved (rarefaction + default)
    • cust.series can now intake multiple factors columns
    • Added example for ecological data
    • Changed taxa to elements
    • boot.matrix, dispRity, summary and plot now also include observed values
    • plot now has an observed option to plot the observed disparity
    • plot option diversity has been renamed elements
  • 2015/10/01 - v0.1.0
    • First release!