NEWS.md
MaximumLength() calculates maximum possible length of characters, including with inapplicable tokensConsistency() now returns retention index and rescaled consistency indexTaxonInfluence() calculates influence of individual taxa on phylogenetic inferenceAdditionTree()
DescendantEdges() for compatibility with ‘TreeTools’ 1.10.0PlotTools::SpectrumLegend() for continuous scales in app.t filesPlotCharacter() now returns invisiblyLengthAdded() 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 namesphylo trees as constraintsQuartetResolution() evaluates how a quartet is resolved in each of a list of treesthrow with stop in C++MinimumLength() fully supports ambiguous applicabilityEasyTrees() ‘shiny’ graphical user interface for tree searchAdditionTree() adds each taxon in sequence to the most parsimonious place on the tree, generating a more parsimonious starting tree than neighbour-joiningPlotCharacter() reconstructs character distributions on treesConstrainedNJ() constructs starting trees that respect a constraintImposeConstraint() reconciles a tree with a constraintSiteConcordance() calculates exact site concordanceConcordantInformation() evaluates signal:noise of dataset implied by a given treePrepareDataProfile() simplifies dataset to allow partial search when multiple applicable tokens are presentResample() conducts bootstrap and jackknife resamplingConsistency() calculates consistency and retention ‘indices’MinimumLength() calculates minimum length of character in a dataset on any tree.TreeLength() supports lists of treesgap =
JackLabels(plot = FALSE)
AsBinary()
nTip parameter in RandomTreeScore() (infer from morphyObj)PhyDatToMatrix(), complementing MatrixToPhyDat()
JackLabels() helper functionMinimumSteps()→MinimumLength() and FitchSteps()→CharacterLength()
message in place of cat, to allow use of suppressMessages()
NyeTreeSimilarity() function implements the tree similarity metric of Nye et al. (2006)MatchingSplitDistance() function implementing the Matching Split distance of Bogdanowicz & Giaro (2012)TreeSplits() is deprecated; use as.Splits() insteadCollapseNodes() and CollapseEdges() allow the creation of polytomiesTree2Splits() lists the bipartition splits implied by a tree topologySplitFrequency() now supports larger treesReadTntTree(), to avoid reliance on generative fileRootTree() allows rooting of tree on incompletely specified or single-taxon outgroupAllTBR() returns all trees one TBR rearrangement awayTBRMoves() reports all possible TBR rearrangementsJackknife() conducts Jackknife resamplingSplitFrequency() reports frequency of clades in a forestSupportColour() allows visual marking of support valuesApeTime() reports the creation date of an ape-exported treeSortTree() flips nodes into a consistent left-right orderAsBinary() supports 0[IW]RatchetConsensus() renamed to [IW]MultiRatchet(), giving a better description of the function’s purposeFitchSteps() now supports datasets with tips not found in treeReadTntTree()
consensus() via ConsensusWithout()
IWRatchetConsensus() now relays concavity value to subsequent functionsReadCharacters() returns labels for all characters and states if character_num = NULL
NJTree() function as shortcut to generate Neighbour-Joining tree from a datasetNNISwap() functions to allow more efficient rearrangement of edgeLists