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

MinimumLength() MinimumSteps()

Minimum length

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