Changelog

Source: NEWS.md

TreeSearch 1.2.0.9000

• New vignette on tree space mapping

TreeSearch 1.2.02022-08-10

• ‘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

TreeSearch 1.1.22022-05-11

• Check tree order & rootedness before scoring (#133)
• Improve error handling
• Replace throw with stop in C++
• Remove test of elapsed times, for CRAN compliance

TreeSearch 1.1.12022-03-22

• 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

TreeSearch 1.1.02022-01-17

• Improvements to ‘shiny’ GUI
• Better integration of rogue taxon exploration
• New vignette describing profile parsimony
• MinimumLength() fully supports ambiguous applicability

TreeSearch 1.0.12021-09-27

• Memory management with invalid input
• Corrections to metadata

TreeSearch 1.0.02021-09-22

New functions

• EasyTrees() ‘shiny’ graphical user interface for tree search
• AdditionTree() adds each taxon in sequence to the most parsimonious place on the tree, generating a more parsimonious starting tree than neighbour-joining
• PlotCharacter() reconstructs character distributions on trees
• ConstrainedNJ() constructs starting trees that respect a constraint
• ImposeConstraint() reconciles a tree with a constraint
• SiteConcordance() calculates exact site concordance
• ConcordantInformation() evaluates signal:noise of dataset implied by a given tree
• PrepareDataProfile() simplifies dataset to allow partial search when multiple applicable tokens are present
• Resample() conducts bootstrap and jackknife resampling
• Consistency() calculates consistency and retention ‘indices’
• MinimumLength() calculates minimum length of character in a dataset on any tree.

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()

TreeSearch 0.4.32020-07-09

• Update tests for compatibility with ‘TreeTools’ v1.1.0
• Improve memory and pointer handling

TreeSearch 0.4.22020-07-07

• Update tests for compatibility with ‘TreeTools’ v1.1.0

TreeSearch 0.4.12020-06-09

• Compatibility with ‘TreeTools’ v1.0.0

TreeSearch 0.4.02020-02-06

New features

• PhyDatToMatrix(), complementing MatrixToPhyDat()
• Documentation with ‘pkgdown’
• JackLabels() helper function

Changes

• Move tree distance measures to new package ‘TreeDist’
• Move tree utility functions to new package ‘TreeTools’
• Rename functions MinimumSteps()→MinimumLength() and FitchSteps()→CharacterLength()

Enhancements

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

TreeSearch 0.3.22019-06-03

• Improve text, content and build speed of vignettes

TreeSearch 0.3.1

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

TreeSearch 0.3.02019-03-21

New features

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

Deprecations

• Function TreeSplits() is deprecated; use as.Splits() instead

Bug fixes

• Correct some mistakes in the documentation

TreeSearch 0.2.22019-01-02

• Correct vignette titles

TreeSearch 0.2.12018-12-07

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

TreeSearch 0.2.02018-09-11

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

TreeSearch 0.1.22018-03-19

• 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

TreeSearch 0.1.02018-03-14

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

TreeSearch 0.0.82018-03-08

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

TreeSearch 0.0.7

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

TreeSearch 0.0.62017-11-07

• First CRAN submission