TreeSearch - v1.6.1

• Handle invariant characters in PolEscapa()
• Handle challenging root positions in PlotCharacter()
• Fix character state colours in app legend
• Tweak documentation

- R
Published by ms609 9 months ago

TreeSearch - v1.6.0

Improvements

• PlotCharacter() performs ancestral state reconstruction on consensus trees (#179)
• Improve support for constraints in AdditionTree() (#173)
• Support for ordered (additive) characters via TreeTools::Decompose()
• Fix SPR behaviour when move is close to root

App improvements

• Buttons to download consensus trees in app
• Fix display of state labels in app

Housekeeping

• Require R 4.0 (to simplify maintenance)

- R
Published by ms609 11 months ago

TreeSearch - v1.5.1

• Fix calls to DescendantEdges()

- R
Published by ms609 almost 2 years ago

TreeSearch - v1.5.0

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

- R
Published by ms609 almost 2 years ago

TreeSearch - v1.4.0

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

- R
Published by ms609 over 2 years ago

TreeSearch - v1.3.2

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

- R
Published by ms609 almost 3 years ago

TreeSearch - v1.3.1

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

- R
Published by ms609 almost 3 years ago

TreeSearch - v1.3.0

New features

• New function LengthAdded() tests which characters contribute to taxon instability, per Pol & Escapa (2009)
• 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 sub-optimal trees
• Use K-means++ clustering

- R
Published by ms609 about 3 years ago

TreeSearch - v1.2.0

• '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.

- R
Published by ms609 over 3 years ago

TreeSearch - v1.1.2

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

- R
Published by ms609 almost 4 years ago

TreeSearch - v1.1.1

• 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

- R
Published by ms609 almost 4 years ago

TreeSearch - v1.1.0

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

- R
Published by ms609 about 4 years ago

TreeSearch - v1.0.1

• Memory management with invalid input
• Corrections to metadata

- R
Published by ms609 over 4 years ago

TreeSearch - v1.0.0

Fundamentally overhauls the search process, with a view to streamlining and simplifying the user's experience.

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()

- R
Published by ms609 over 4 years ago

TreeSearch - v0.4.3

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

- R
Published by ms609 over 5 years ago

TreeSearch - v0.4.2

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

- R
Published by ms609 over 5 years ago

TreeSearch - v0.4.1

• Compatibility with 'TreeTools' v1.0.0

- R
Published by ms609 over 5 years ago

TreeSearch - 0.4.0

New features

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

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()

- R
Published by ms609 about 6 years ago

TreeSearch - 0.3.2

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)

Enhancements

• Improve text, content and build speed of vignettes

Bug fixes

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

- R
Published by ms609 over 6 years ago

TreeSearch - 0.3.0

New features

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

Deprecations

• Function TreeSplits is deprecated; use Tree2Splits instead.

Bug fixes

• Correct some mistakes in the documentation

- R
Published by ms609 almost 7 years ago

TreeSearch - 0.2.2

Bug fixes

• Correct vignette titles

- R
Published by ms609 about 7 years ago

TreeSearch - 0.2.1

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

- R
Published by ms609 about 7 years ago

TreeSearch - 0.2.0

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

- R
Published by ms609 over 7 years ago

TreeSearch - 0.1.2

Avoid miscellaneous C and R warnings:

• 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

- R
Published by ms609 almost 8 years ago

TreeSearch - 0.1.0

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

- R
Published by ms609 almost 8 years ago

TreeSearch - 0.0.8

TreeSearch 0.0.8

New functions

• 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

- R
Published by ms609 almost 8 years ago