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NEWS.md

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TreeSearch 1.5.1.9000 (2024-10)

  • Fix display of state labels in app

TreeSearch 1.5.1 (2024-05-23)

  • Fix calls to DescendantEdges()

TreeSearch 1.5.0 (2024-04-03)

  • MaximumLength() calculates maximum possible length of characters, including with inapplicable tokens
  • Consistency() now returns retention index and rescaled consistency index

TreeSearch 1.4.0 (2023-08-18)

New features

  • TaxonInfluence() calculates influence of individual taxa on phylogenetic inference

Search improvements

  • Default to use equal weighting during ratchet iterations
  • Support null constraints in AdditionTree()

App improvements

  • Exclude taxa from search in app
  • Allow search to continue when loading a new file with different taxon names into the app

Housekeeping

  • Update calls to DescendantEdges() for compatibility with 'TreeTools' 1.10.0

TreeSearch 1.3.2 (2023-04-27)

  • Use PlotTools::SpectrumLegend() for continuous scales in app
  • Restore auto-termination of .t files

TreeSearch 1.3.1 (2023-03-29)

  • PlotCharacter() now returns invisibly
  • Fix missing character in Wills 2012 dataset
  • Search by character text in GUI
  • Call C functions using symbols

TreeSearch 1.3.0 (2023-02-20)

New features

  • New function LengthAdded() tests which characters contribute to taxon instability, per Pol & Escapa (2009), doi:10.1111/j.1096-0031.2009.00258.x
  • WhenFirstHit() recovers tree search information from tree names
  • New vignette on tree space mapping
  • Support phylo trees as constraints

GUI improvements

  • Support reading characters from Excel spreadsheets
  • Allow retention of suboptimal trees
  • Use K-means++ clustering

TreeSearch 1.2.0 (2022-07-35)

  • '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 1.1.2 (2022-05-11)

  • 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 1.1.1 (2022-03-22)

  • 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 1.1.0 (2022-01-17)

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

TreeSearch 1.0.1 (2021-09-27)

  • Memory management with invalid input
  • Corrections to metadata

TreeSearch 1.0.0 (2021-09-21)

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 0.4.3 (2020-07-09)

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

TreeSearch 0.4.2 (2020-07-07)

  • Update tests for compatibility with 'TreeTools' v1.1.0

TreeSearch 0.4.1 (2020-06-09)

  • Compatibility with 'TreeTools' v1.0.0

TreeSearch 0.4.0 (2020-02-06)

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 0.3.2 (2019-06-03)

  • 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 0.3.0 (2019-03-21)

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 0.2.2 (2019-01-02)

  • Correct vignette titles

TreeSearch 0.2.1 (2018-12-07)

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 0.2.0 (2018-09-10)

New features

  • RootTree() 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 0.1.2 (2018-03-20)

  • 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 0.1.0 (2018-03-14)

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 0.0.8

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

Inapplicable tokens:

  • 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 0.0.6

  • First CRAN submission