Changelog

Source: NEWS.md

TreeSearch 1.5.1 (2024-05-23)

CRAN release: 2024-05-23

• Fix calls to DescendantEdges()

TreeSearch 1.5.0 (2024-04-03)

CRAN release: 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)

CRAN release: 2023-08-26

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)

CRAN release: 2023-04-27

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

TreeSearch 1.3.1 (2023-03-29)

CRAN release: 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)

CRAN release: 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)

CRAN release: 2022-08-10

• ‘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 1.1.2 (2022-05-11)

CRAN release: 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)

CRAN release: 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)

CRAN release: 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)

CRAN release: 2021-09-27

• Memory management with invalid input
• Corrections to metadata

TreeSearch 1.0.0 (2021-09-21)

CRAN release: 2021-09-22

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 0.4.3 (2020-07-09)

CRAN release: 2020-07-09

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

TreeSearch 0.4.2 (2020-07-07)

CRAN release: 2020-07-07

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

TreeSearch 0.4.1 (2020-06-09)

CRAN release: 2020-06-09

• Compatibility with ‘TreeTools’ v1.0.0

TreeSearch 0.4.0 (2020-02-06)

CRAN release: 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)

CRAN release: 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)

CRAN release: 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)

CRAN release: 2019-01-02

• Correct vignette titles

TreeSearch 0.2.1 (2018-12-07)

CRAN release: 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)

CRAN release: 2018-09-11

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)

CRAN release: 2018-03-19

• 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 0.1.0 (2018-03-14)

CRAN release: 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

CRAN release: 2018-03-08

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

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

CRAN release: 2017-11-07

• First CRAN submission