Function reference • TreeSearch

Custom search Functions to search for optimal phylogenetic trees.
`Jackknife()`	Jackknife resampling
`MorphyBootstrap()` `Ratchet()` `MultiRatchet()` `RatchetConsensus()`	Parsimony Ratchet
Tree scoring Functions that provide tree scores, for optimization.
`CharacterLength()` `FitchSteps()` `FastCharacterLength()`	Character length
`LengthAdded()` `PolEscapa()`	Contribution of character to leaf instability
`MinimumLength()` `MinimumSteps()` `MaximumLength()`	Minimum and Maximum lengths possible for a character
`TaxonInfluence()`	Rank taxa by their influence on phylogenetic results
`IWScore()` `TreeLength()` `Fitch()`	Calculate the parsimony score of a tree given a dataset
`ConcordantInformation()` `Evaluate()` `ConcordantInfo()`	Evaluate the concordance of information between a tree and a dataset
`Consistency()`	Consistency / retention "indices"
`PlotCharacter()`	Plot the distribution of a character on a tree
`RandomTreeScore()`	Parsimony score of random postorder tree
Split support Functions that calculate node support.
`JackLabels()`	Label nodes with jackknife support values
`Jackknife()`	Jackknife resampling
`MaximizeParsimony()` `Resample()` `EasyTrees()` `EasyTreesy()`	Find most parsimonious trees
`QuartetConcordance()` `ClusteringConcordance()` `PhylogeneticConcordance()` `MutualClusteringConcordance()` `SharedPhylogeneticConcordance()`	Calculate site concordance factor
Tree (re)construction Tree generation and rearrangement functions.
`AdditionTree()`	Addition tree
`RandomMorphyTree()`	Random postorder tree
`NNI()` `cNNI()` `NNISwap()` `RootedNNI()` `RootedNNISwap()`	Nearest neighbour interchange (NNI)
`AllSPR()`	All SPR trees
`SPR()` `SPRMoves()` `SPRSwap()` `RootedSPR()` `RootedSPRSwap()`	Subtree pruning and rearrangement (SPR)
`cSPR()`	`cSPR()` expects a tree rooted on a single tip.
`TBR()` `TBRMoves()` `TBRSwap()` `RootedTBR()` `RootedTBRSwap()`	Tree bisection and reconnection (TBR)
`RearrangeEdges()`	Rearrange edges of a phylogenetic tree
Profile parsimony Functions to help calculate profile parsimony scores.
`Carter1()` `Log2Carter1()` `LogCarter1()`	Number of trees with m steps
`PrepareDataProfile()` `PrepareDataIW()`	Prepare data for Profile Parsimony
`StepInformation()`	Information content of a character known to contain e steps
`WithOneExtraStep()`	Number of trees with one extra step
`profiles`	Empirically counted profiles for small trees
Morphy APIs Functions that interface with the Morphy C library.
`GapHandler()`	Read how a Morphy Object handles the inapplicable token
`MorphyWeights()` `SetMorphyWeights()`	Set and get the character weightings associated with a Morphy object.
`PhyDat2Morphy()`	Initialize a Morphy object from a `phyDat` object
`SingleCharMorphy()`	Morphy object from single character
`UnloadMorphy()`	Destroy a Morphy object
`is.morphyPtr()`	Is an object a valid Morphy object?
`summary(<morphyPtr>)`	Details the attributes of a morphy object
Datasets Data that accompanies the package.
`congreveLamsdellMatrices`	100 simulated data matrices
`inapplicable.datasets` `inapplicable.phyData` `inapplicable.trees` `inapplicable.citations`	Thirty datasets with inapplicable data
`profiles`	Empirically counted profiles for small trees
`referenceTree`	Tree topology for matrix simulation
Utility functions Miscellaneous functions used within the package.
`ClusterStrings()`	Cluster similar strings
`QuartetResolution()`	Relationship between four taxa
`WhenFirstHit()`	When was a tree topology first hit?

Reference

Custom search

Tree scoring

Split support

Tree (re)construction

Profile parsimony

Morphy APIs

Datasets

Utility functions