# Phylogenetic Analysis with Discrete Character Data

## Documentation for package ‘TreeSearch’ version 1.3.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

AdditionTree | Addition tree
AllSPR | All SPR trees
Carter1 | Number of trees with _m_ steps
CharacterLength | Character length
ClusteringConcordance | Calculate site concordance factor
ClusterStrings | Cluster similar strings
cNNI | Nearest neighbour interchange (NNI)
ConcordantInfo | Evaluate the concordance of information between a tree and a dataset
ConcordantInformation | Evaluate the concordance of information between a tree and a dataset
congreveLamsdellMatrices | 100 simulated data matrices
Consistency | Consistency / retention "indices"
cSPR | 'cSPR()' expects a tree rooted on a single tip.
EasyTrees | Find most parsimonious trees
EasyTreesy | Find most parsimonious trees
Evaluate | Evaluate the concordance of information between a tree and a dataset
FastCharacterLength | Character length
Fitch | Calculate the parsimony score of a tree given a dataset
FitchSteps | Character length
GapHandler | Read how a Morphy Object handles the inapplicable token
inapplicable.citations | Thirty datasets with inapplicable data
inapplicable.datasets | Thirty datasets with inapplicable data
inapplicable.phyData | Thirty datasets with inapplicable data
inapplicable.trees | Thirty datasets with inapplicable data
is.morphyPtr | Is an object a valid Morphy object?
IWScore | Calculate the parsimony score of a tree given a dataset
Jackknife | Jackknife resampling
JackLabels | Label nodes with jackknife support values
LengthAdded | Contribution of character to leaf instability
Log2Carter1 | Number of trees with _m_ steps
LogCarter1 | Number of trees with _m_ steps
MaximizeParsimony | Find most parsimonious trees
MinimumLength | Minimum length
MinimumLength.character | Minimum length
MinimumLength.numeric | Minimum length
MinimumLength.phyDat | Minimum length
MinimumSteps | Minimum length
MorphyBootstrap | Parsimony Ratchet
MorphyWeights | Set and get the character weightings associated with a Morphy object.
MultiRatchet | Parsimony Ratchet
MutualClusteringConcordance | Calculate site concordance factor
NNI | Nearest neighbour interchange (NNI)
NNISwap | Nearest neighbour interchange (NNI)
PhyDat2Morphy | Initialize a Morphy object from a 'phyDat' object
PhylogeneticConcordance | Calculate site concordance factor
PlotCharacter | Plot the distribution of a character on a tree
PolEscapa | Contribution of character to leaf instability
PrepareDataIW | Prepare data for Profile Parsimony
PrepareDataProfile | Prepare data for Profile Parsimony
profiles | Empirically counted profiles for small trees
QuartetConcordance | Calculate site concordance factor
QuartetResolution | Relationship between four taxa
RandomMorphyTree | Random postorder tree
RandomTreeScore | Parsimony score of random postorder tree
Ratchet | Parsimony Ratchet
RatchetConsensus | Parsimony Ratchet
RearrangeEdges | Rearrange edges of a phylogenetic tree
referenceTree | Tree topology for matrix simulation
Resample | Find most parsimonious trees
RootedNNI | Nearest neighbour interchange (NNI)
RootedNNISwap | Nearest neighbour interchange (NNI)
RootedSPR | Subtree pruning and rearrangement (SPR)
RootedSPRSwap | Subtree pruning and rearrangement (SPR)
RootedTBR | Tree bisection and reconnection (TBR)
RootedTBRSwap | Tree bisection and reconnection (TBR)
SetMorphyWeights | Set and get the character weightings associated with a Morphy object.
SharedPhylogeneticConcordance | Calculate site concordance factor
SingleCharMorphy | Morphy object from single character
SiteConcordance | Calculate site concordance factor
SPR | Subtree pruning and rearrangement (SPR)
SPRMoves | Subtree pruning and rearrangement (SPR)
SPRMoves.matrix | Subtree pruning and rearrangement (SPR)
SPRMoves.phylo | Subtree pruning and rearrangement (SPR)
SPRSwap | Subtree pruning and rearrangement (SPR)
StepInformation | Information content of a character known to contain _e_ steps
summary.morphyPtr | Details the attributes of a morphy object
TBR | Tree bisection and reconnection (TBR)
TBRMoves | Tree bisection and reconnection (TBR)
TBRMoves.matrix | Tree bisection and reconnection (TBR)
TBRMoves.phylo | Tree bisection and reconnection (TBR)
TBRSwap | Tree bisection and reconnection (TBR)
TreeLength | Calculate the parsimony score of a tree given a dataset
TreeLength.list | Calculate the parsimony score of a tree given a dataset
TreeLength.multiPhylo | Calculate the parsimony score of a tree given a dataset
TreeLength.numeric | Calculate the parsimony score of a tree given a dataset
TreeLength.phylo | Calculate the parsimony score of a tree given a dataset
UnloadMorphy | Destroy a Morphy object
WhenFirstHit | When was a tree topology first hit?
WithOneExtraStep | Number of trees with one extra step