# Phylogenetic Tree Search Using Custom Optimality Criteria

## Documentation for package ‘TreeSearch’ version 0.3.0

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

## Help Pages

A B C D E F I J L M N P R S T U V W

## -- A --

AddTip | Add a tip to a phylogenetic tree
AllAncestors | List all ancestral nodes
AllDescendantEdges | Descendant Edges
AllSplitPairings | All split pairings
AllSPR | All SPR trees
AllTBR | TBR
ApeTime | Ape Time
AsBinary | Convert a number to binary

## -- B --

brewer | Brewer palettes

## -- C --

CollapseEdge | Collapse nodes on a phylogenetic tree
CollapseNode | Collapse nodes on a phylogenetic tree
congreveLamsdellMatrices | 100 simulated data matrices
ConsensusWithout | Consensus without taxa

## -- D --

DescendantEdges | Descendant Edges
DoubleFactorial | Double Factorial
doubleFactorials | Double factorials
DropSingleSplits | Drop Single Splits

## -- E --

EdgeAncestry | EdgeAncestry
EnforceOutgroup | Force taxa to form an outgroup
Entropy | Entropy in bits
Evaluate | Evaluate tree

## -- F --

Fitch | Calculate parsimony score with inapplicable data
FitchSteps | Fitch score
ForestSplits | Frequency of splits

## -- I --

IC1Spr | Number of trees one SPR step away Formula given by Allen and Steel (2001).
ICSteps | Information Content Steps
inapplicable.citations | Thirty Datasets with Inapplicable data
inapplicable.datasets | Thirty Datasets with Inapplicable data
inapplicable.phyData | Thirty Datasets with Inapplicable data
InfoAmounts | Amount of information in each character
IWBootstrap | Ratchet bootstrapper
IWDestroyMorphy | Implied weights parsimony Score
IWInitMorphy | Implied weights parsimony Score
IWScore | Implied weights parsimony Score
IWScoreMorphy | Profile Parsimony Score

## -- J --

JointInformation | Joint Information of two splits

## -- L --

LnRooted | Number of rooted/unrooted trees These functions return the number of rooted or unrooted trees consistent with a given pattern of splits.
LnSplitMatchProbability | Probability of matching this well
LnUnrooted | Number of rooted/unrooted trees These functions return the number of rooted or unrooted trees consistent with a given pattern of splits.
LnUnrootedMult | Number of rooted/unrooted trees These functions return the number of rooted or unrooted trees consistent with a given pattern of splits.
LnUnrootedSplits | Number of rooted/unrooted trees These functions return the number of rooted or unrooted trees consistent with a given pattern of splits.
Lobo.data | Raw data from Zhang et al. 2016
Lobo.phy | Data from Zhang et al. 2016 in phyDat format
LogDoubleFactorial | Double Factorial
LogDoubleFactorial.int | Double Factorial
logDoubleFactorials | Natural logarithms of double factorials
LogisticPoints | Logistic Points Extract points from a fitted model
LogTreesConsistentWithTwoSplits | Mutual information of two splits
LogTreesMatchingSplit | Number of trees matching a bipartition split

## -- M --

MarkMissing | Consensus without taxa
MatrixToList | Edge matrix to edge list
MinimumSteps | Minimum steps
MorphyBootstrap | Ratchet bootstrapper
MorphyWeights | Report the character weightings associated with a Morphy object
MultiSplitInformation | Information content of a split
MutualArborealInfo | Information-based generalized Robinson-Foulds distance between two trees
MutualArborealInfoSplits | Information-based generalized Robinson-Foulds distance between two trees
MutualClusterInfo | Information-based generalized Robinson-Foulds distance between two trees
MutualClusterInfoSplits | Information-based generalized Robinson-Foulds distance between two trees

## -- N --

N1Spr | Number of trees one SPR step away Formula given by Allen and Steel (2001).
NewickTree | Newick Tree
NJTree | Neighbour Joining Tree
NNI | NNI
NNISwap | NNI
NPartitionPairs | Distributions of taxa consistent with a partition pair.
NRooted | Number of rooted/unrooted trees These functions return the number of rooted or unrooted trees consistent with a given pattern of splits.
NUnrooted | Number of rooted/unrooted trees These functions return the number of rooted or unrooted trees consistent with a given pattern of splits.
NUnrootedMult | Number of rooted/unrooted trees These functions return the number of rooted or unrooted trees consistent with a given pattern of splits.
NUnrootedSplits | Number of rooted/unrooted trees These functions return the number of rooted or unrooted trees consistent with a given pattern of splits.

## -- P --

PhyDat | Read characters from Nexus file
PhyDat2Morphy | Initialize a Morphy Object from a phyDat object
PhyToString | Extract character data from a phyDat object as a string
PrepareDataIW | Prepare data for Profile Parsimony
PrepareDataProfile | Prepare data for Profile Parsimony
ProfileBootstrap | Ratchet bootstrapper
ProfileDestroyMorphy | Profile Parsimony Score
ProfileInitMorphy | Profile Parsimony Score
ProfileScore | Profile Parsimony Score
ProfileScoreMorphy | Profile Parsimony Score

## -- R --

RandomMorphyTree | Random postorder tree
RandomTree | Generate random tree topology from dataset
RandomTreeScore | Parsimony score of random postorder tree
ReadAsPhyDat | Read characters from Nexus file
ReadCharacters | Read characters from Nexus file
ReadTntAsPhyDat | Read characters from Nexus file
ReadTntCharacters | Read characters from Nexus file
ReadTntTree | Parse TNT Tree
RearrangeEdges | Rearrange edges of a phylogenetic tree
referenceTree | Tree topology for matrix simulation
Renumber | Renumber a tree's nodes and tips
RenumberTips | Reorder tips
RootedNNI | NNI
RootedNNISwap | NNI
RootedSPR | Subtree Pruning and Rearrangement
RootedSPRSwap | Subtree Pruning and Rearrangement
RootedTBR | TBR
RootedTBRSwap | TBR
RootTree | Root Tree on specified tips

## -- S --

SetMorphyWeights | Set the character weightings associated with a Morphy object
SingleCharMorphy | Morphy object from single character
SingleTaxonTree | SingleTaxonTree
SortTree | Sort tree
SplitEntropy | Entropy of two splits
SplitFrequency | Frequency of splits
SplitInformation | Information content of a split
SplitMatchProbability | Probability of matching this well
SplitMutualInformation | Mutual information of two splits
SplitNumber | Frequency of splits
SplitPairingInformationIndex | All split pairings
SplitsCompatible | Are splits compatible?
SplitVariationOfInformation | Mutual information of two splits
SPR | Subtree Pruning and Rearrangement
SPRSwap | Subtree Pruning and Rearrangement
StringToPhyDat | String to phyDat
StringToPhydat | String to phyDat
Subtree | Extract subtree
SuccessiveApproximations | Tree Search using Successive Approximations
summary.morphyPtr | Details the attributes of a morphy object
SupportColor | Support colour
SupportColour | Support colour

## -- T --

TBR | TBR
TBRMoves | TBR
TBRSwap | TBR
TNTText2Tree | Parse TNT Tree
TreesConsistentWithTwoSplits | Mutual information of two splits
TreesMatchingSplit | Number of trees matching a bipartition split
TreeSplits | Frequency of splits

## -- U --

UniqueSplits | Unique Splits
UnloadMorphy | Destroy a Morphy Object
UnloadTreeSearch | Unload this library
UnrootedTreesMatchingSplit | Number of trees consistent with split

## -- V --

VariationOfArborealInfo | Information-based generalized Robinson-Foulds distance between two trees
VariationOfArborealInfoSplits | Information-based generalized Robinson-Foulds distance between two trees

## -- W --

WithOneExtraStep | Number of trees with one extra step