NEWS.txt

CHANGES IN CLADDIS VERSION 0.2

  NEW FEATURES
    o Added citation file to package. Please cite this paper whenever you use Claddis.
    o Added character changes output to DiscreteCharacterRate function.
    o Added internal and terminal branch versions of the time series output for DiscreteCharacterRate. This was added to complete the internal and terminal test and was used as an additional set of sensitivity tests in Close et al. (2015).
    o Added new ChronoPhyloMorphospacePlot function to make three-dimensional plots of two ordination axes against time.
    o Added new CompactifyMatrix function for collapsing redundant characters.
    o Added new DolloSCM function for producing stochastic Dollo character maps.
    o Added new MakeMorphMatrix function to create Claddis formatted data from within R.
    o Added new MatrixPruner function to safely remove characters or taxa from discrete character-taxon matrices.
    o Added new MorphDistMatrixFast function for producing faster distance matrices.
    o Added new MorphMatrix2PCoA function for performing principal coordinates analysis on cladistic data sets.
    o Added new MorphospacePlot function for performing basic morphospace plots from MorphMatrix2PCoA output.
    o Added new MultiMorphospacePlot function for performing plots of multiple axes from MorphMatrix2PCoA output.
    o Added new StackPlot function for plotting time-sliced ordination spaces as a vertical stack (oldest at bottom, youngest at top).
    o Added new WriteMorphNexus function for writing character data out to #NEXUS format.
    o Added new WriteMorphTNT function for writing character data out to TNT format.
    o Added this NEWS file to keep users abreast of changes to Claddis.

  BUG FIXES
    o Fixed bug in MorphDistMatri where GED values were not taking into account differentially weighted data (thanks to Thomas Guillerme).
    o Fixed minor bugs in ReadMorphNexus, for example, where a taxon name includes the string "matrix". This would have caused errors previously.
    o Fixed bug in output from SafeTaxonomicReduction that stops matrices being converted to vectors (thanks to Dave Bapst).
    o Removed random seed file that could corrupt stochastic functions (thanks to Dave Bapst). This should not have caused problems as no core functions are stochastic at present.
    o Removed duplicated line in AncEstMatrix (thanks to Thomas Guillerme). This should speed up this function and the main rate function which calls it, but should not have lead to any actual errors.

  OTHER CHANGES
    o Added reference to Close et al. (2015): technically the first published paper to use Claddis itself. (Older papers made use of earlier versions of the core functions.)
    o Added warning to help file for CorrectRootTime to tell user that this can only be used for trees of minimally three taxa (thanks to Dave Bapst). This is really an edge case issue, but for some other functions trees with two taxa are allowed.
    o Added warning to help file for SafeTaxonomicReduction about inapplicable states being treated as missing states. As far as I know this is an issue for the approach in general that has not been properly investigated yet.
    o Changes made to how functions are imported to meet the new CRAN upload rules.
    o Converted entire package to Roxygen. This should not affect the user experience at all.
    o Fixed typo in Yang et al. (1995) citation.
    o Made some minor internal changes to deal with the new phytools formatted output from make.simmap.
    o Removed an .Rhistory file that was accidentally being included in the tarball.