AddTip                  Add a tip to a phylogenetic tree
AllAncestors            List all ancestral nodes
AllSPR                  All SPR trees
AllSplitPairings        All split pairings
ApeTime                 Ape Time
AsBinary                Convert a number to binary
CollapseNode            Collapse nodes on a phylogenetic tree
ConsensusWithout        Consensus without taxa
DescendantEdges         Descendant Edges
DoubleFactorial         Double Factorial
DropSingleSplits        Drop Single Splits
EdgeAncestry            EdgeAncestry
EnforceOutgroup         Force taxa to form an outgroup
Entropy                 Entropy in bits
Evaluate                Evaluate tree
Fitch                   Calculate parsimony score with inapplicable
                        data
FitchSteps              Fitch score
ICSteps                 Information Content Steps
IWScore                 Implied weights parsimony Score
IWScoreMorphy           Profile Parsimony Score
InfoAmounts             Amount of information in each character
JointInformation        Joint Information of two splits
Lobo.data               Raw data from Zhang et al. 2016
Lobo.phy                Data from Zhang et al. 2016 in phyDat format
LogisticPoints          Logistic Points Extract points from a fitted
                        model
MatrixToList            Edge matrix to edge list
MinimumSteps            Minimum steps
MorphyBootstrap         Ratchet bootstrapper
MorphyWeights           Report the character weightings associated with
                        a Morphy object
MutualArborealInfo      Information-based generalized Robinson-Foulds
                        distance between two trees
N1Spr                   Number of trees one SPR step away Formula given
                        by Allen and Steel (2001).
NJTree                  Neighbour Joining Tree
NNI                     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.
NewickTree              Newick Tree
PhyDat2Morphy           Initialize a Morphy Object from a phyDat object
PhyToString             Extract character data from a phyDat object as
                        a string
PrepareDataProfile      Prepare data for Profile Parsimony
RandomMorphyTree        Random postorder tree
RandomTree              Generate random tree topology from dataset
RandomTreeScore         Parsimony score of random postorder tree
ReadCharacters          Read characters from Nexus file
ReadTntTree             Parse TNT Tree
RearrangeEdges          Rearrange edges of a phylogenetic tree
Renumber                Renumber a tree's nodes and tips
RenumberTips            Reorder tips
RootTree                Root Tree on specified tips
SPR                     Subtree Pruning and Rearrangement
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
SplitsCompatible        Are splits compatible?
StringToPhyDat          String to phyDat
Subtree                 Extract subtree
SuccessiveApproximations
                        Tree Search using Successive Approximations
SupportColour           Support colour
TBR                     TBR
TreesMatchingSplit      Number of trees matching a bipartition split
UniqueSplits            Unique Splits
UnloadMorphy            Destroy a Morphy Object
UnloadTreeSearch        Unload this library
UnrootedTreesMatchingSplit
                        Number of trees consistent with split
WithOneExtraStep        Number of trees with one extra step
brewer                  Brewer palettes
congreveLamsdellMatrices
                        100 simulated data matrices
doubleFactorials        Double factorials
inapplicable.citations
                        Thirty Datasets with Inapplicable data
inapplicable.datasets   Thirty Datasets with Inapplicable data
inapplicable.phyData    Thirty Datasets with Inapplicable data
logDoubleFactorials     Natural logarithms of double factorials
referenceTree           Tree topology for matrix simulation
summary.morphyPtr       Details the attributes of a morphy object
