Package index • TreeSearch

Custom search

Functions to search for optimal phylogenetic trees.

Jackknife(): Jackknife resampling
MorphyBootstrap() Ratchet() MultiRatchet() RatchetConsensus(): Parsimony Ratchet

Functions that provide tree scores, for optimization.

CharacterLength() FastCharacterLength(): Character length
ExpectedLength(): Expected 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

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

Functions that calculate support for edges.

JackLabels(): Label nodes with jackknife support values
Jackknife(): Jackknife resampling
MaximizeParsimony() Resample() EasyTrees() EasyTreesy(): Find most parsimonious trees
MostContradictedFreq(): Frequency of most common contradictory split
PresCont(): Group present or contradicted score
QuartetConcordance() ClusteringConcordance() PhylogeneticConcordance() MutualClusteringConcordance() SharedPhylogeneticConcordance(): Calculate site concordance factor

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

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

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

Miscellaneous functions used within the package.