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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?