NEWS.md
throw
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()
TreeSplits()
is deprecated; use as.Splits()
insteadCollapseNodes
and CollapseEdges
allow the creation of polytomiesTree2Splits
lists the bipartition splits implied by a tree topologyRootTree
function 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()
NJTree()
function as shortcut to generate Neighbour-Joining tree from a datasetNNISwap()
functions to allow more efficient rearrangement of edgeLists