• New vignette on tree space mapping
  • ‘shiny’ GUI improvements:
    • Export log of tree search commands
    • Export R scripts to reproduce figures
    • Simplify layout
    • Misc bug fixes
  • New function QuartetResolution() evaluates how a quartet is resolved in each of a list of trees
  • Check tree order & rootedness before scoring (#133)
  • Improve error handling
  • Replace throw with stop in C++
  • Remove test of elapsed times, for CRAN compliance
  • GUI allows selection of subset of trees, for easier analysis of Bayesian tree sets
  • Miscellaneous fixes and improvements in ‘shiny’ GUI
  • Test suite for ‘shiny’ GUI
  • Update tests for TreeSearch 1.7
  • Improvements to ‘shiny’ GUI
  • Better integration of rogue taxon exploration
  • New vignette describing profile parsimony
  • MinimumLength() fully supports ambiguous applicability
  • Memory management with invalid input
  • Corrections to metadata

New functions

Improvements

  • TreeLength() supports lists of trees
  • Set handling of ‘gap’ token (-) when creating Morphy object with gap =
  • Label nodes with split frequencies using JackLabels(plot = FALSE)
  • Support for topological constraints during tree search
  • Remove redundant function AsBinary()
  • Drop nTip parameter in RandomTreeScore() (infer from morphyObj)
  • C implementations of rearrangement functions
  • Improved command line interface for search progress messaging

Deprecations

  • Remove redundant internal function LogisticPoints()
  • Update tests for compatibility with ‘TreeTools’ v1.1.0
  • Improve memory and pointer handling
  • Update tests for compatibility with ‘TreeTools’ v1.1.0
  • Compatibility with ‘TreeTools’ v1.0.0

New features

Changes

Enhancements

  • Improve speed of tests (by increasing probability of false positives)
  • Use message in place of cat, to allow use of suppressMessages()
  • Improve text, content and build speed of vignettes

New features

  • NyeTreeSimilarity() function implements the tree similarity metric of Nye et al. (2006)
  • MatchingSplitDistance() function implementing the Matching Split distance of Bogdanowicz & Giaro (2012)

Bug fixes

  • Check whether input tree is bifurcating before attempting rearrangements, to avoid crashes on unsupported input

New features

  • Implement an information theoretic tree distance measure (Smith, 2020)
  • Prepare for new random number generator in R3.6.0

Deprecations

Bug fixes

  • Correct some mistakes in the documentation
  • Correct vignette titles

New features

  • CollapseNodes and CollapseEdges allow the creation of polytomies
  • Tree2Splits lists the bipartition splits implied by a tree topology

Enhancements

  • SplitFrequency now supports larger trees
  • Can specify tip labels directly to ReadTntTree, to avoid reliance on generative file

Bug fixes

  • Export missing functions

New features

  • RootTree function allows rooting of tree on incompletely specified or single-taxon outgroup
  • AllTBR returns all trees one TBR rearrangement away
  • TBRMoves reports all possible TBR rearrangements
  • Jackknife conducts Jackknife resampling
  • SplitFrequency reports frequency of clades in a forest
  • SupportColour allows visual marking of support values
  • ApeTime reports the creation date of an ape-exported tree
  • SortTree flips nodes into a consistent left-right order
  • AsBinary supports 0

Enhancements

  • [IW]RatchetConsensus() renamed to [IW]MultiRatchet(), giving a better description of the function’s purpose
  • Don’t warn about missing EOL when reading Nexus or TNT files
  • Add new 12-colour colourblind-friendly palette
  • FitchSteps() now supports datasets with tips not found in tree
  • Improve portability of function ReadTntTree()

Bug fixes

  • [IW]MultiRatchet() now considers trees identical even if they’ve been hit a different number of times
  • Update MorphyLib library to fix C warnings
  • Remove non-ASCII characters from data
  • Disable slow-building and problematic vignette
  • Use local copy of citation style when building vignettes

New features

  • Helper functions to read Nexus and TNT data and trees
  • Brewer palette in local data to allow easier colouring

Enhancements

  • Allow additional parameters to be passed to consensus via ConsensusWithout

Bug fixes

  • C11 compliance
  • IWRatchetConsensus now relays concavity value to subsequent functions
  • ReadCharacters returns labels for all characters and states if character_num = NULL

New features

  • Added NJTree() function as shortcut to generate Neighbour-Joining tree from a dataset
  • Add functions to allow recovery of all trees one rearrangement from that input

Efficiency gains

  • Separate out NNISwap() functions to allow more efficient rearrangement of edgeLists
  • [9002] Improve efficiency by using three-pass algorithm in place of four-pass precursor
  • [9004] Bootstrap search improvements

Bug fixes

  • [9003] User now able to specify value of concavity constant (was overridden to k = 4)
  • [9003] Bootstrap replicates now scored correctly (and without warning) under implied weights

Inapplicables:

  • Integrated with this package (previously in inapplicable)
  • Handle inapplicable data via API to Martin Brazeau’s Morphy Phylogenetic Library

Profile Parsimony:

  • Integrated with this package (previously in ProfileParsimony)
  • Faster calculation of concavity profiles in C
  • Persistent memoization with R.cache
  • First CRAN submission