Man pages for TreeSearch
Phylogenetic Tree Search Using Custom Optimality Criteria

AddTipAdd a tip to a phylogenetic tree
AllAncestorsList all ancestral nodes
AllSPRAll SPR trees
AncestorEdgeAncestral edge
ApeTimeApe Time
AsBinaryConvert a number to binary
brewerBrewer palettes
CladeSizesClade sizes
CladewiseReorder tree Cladewise
C_node_depthNode depth Wrapper for the ape function
CollapseNodeCollapse nodes on a phylogenetic tree
congreveLamsdellMatrices100 simulated data matrices
ConsensusWithoutConsensus without taxa
DescendantEdgesDescendant Edges
DFactDouble factorial
DoubleNNIDouble NNI
DropSingleSplitsDrop Single Splits
EnforceOutgroupForce taxa to form an outgroup
EvaluateEvaluate tree
ExtractTaxaExtract taxa from a matrix block
FitchCalculate parsimony score with inapplicable data
FitchStepsFitch score
ICPerStepInformation content per step
ICStepsInformation Content Steps
inapplicable.citationsThirty Datasets with Inapplicable data
inapplicable.datasetsThirty Datasets with Inapplicable data
inapplicable.phyDataThirty Datasets with Inapplicable data
InfoAmountsAmount of information in each character
IWScoreImplied weights parsimony Score
LDFactLog double factorial Handles odd and even inout numbers
LDFactorialLog double factorial
ListToMatrixEdge list to edge matrix
Lobo.dataRaw data from Zhang et al. 2016
Lobo.phyData from Zhang et al. 2016 in phyDat format
LogisticPointsLogistic Points Extract points from a fitted model
MatrixToListEdge matrix to edge list
MatrixToPhyDatMatrix to phydat
MinimumStepsMinimum steps
MorphyBootstrapRatchet bootstrapper
MorphyErrorCheckCheck for error whilst modifying Morphy object
MorphyTreeLengthCalculate parsimony score with inapplicable data
MorphyWeightsReport the character weightings associated with a Morphy...
mpl_apply_tipdataCommits parameters prior to nodal set calculations.
mpl_attach_rawdataAttach raw character state data (i.e. tip data).
mpl_attach_symbolsAttach a caller-specified list of symbols.
mpl_delete_MorphyDestroys an instance of a Morphy object.
mpl_delete_rawdataDeletes the caller-input data.
mpl_first_down_reconReconstructs the first (downpass) nodal reconstructions
mpl_first_up_reconReconstructs the second (uppass) nodal reconstructions.
mpl_get_charac_weightRetrieve the weight of a character in the dataset
mpl_get_num_characRetrieve the number of character (columns) in the dataset.
mpl_get_num_internal_nodesGets the number of internal nodal reconstruction sets being...
mpl_get_numtaxaRetrieve the number of taxa (rows) in the dataset.
mpl_get_symbolsRetrieves the current list of symbols.
mpl_init_MorphySets up the dimensions of the dataset.
mpl_new_MorphyCreates a new instance of a Morphy object
mpl_second_down_reconPerforms the second nodal reconstructions for characters with...
mpl_second_up_reconFinalises the ancestral state reconstructions for characters...
mpl_set_charac_weightSet the weight of a character in the dataset
mpl_set_num_internal_nodesSets the number of internal nodes in the dataset
mpl_set_parsim_tSets a character's parsimony function type
mpl_translate_errorConverts a numeric error code to human-readable format
mpl_update_lower_rootUpdates the nodal sets for a lower ('dummy') root node
mpl_update_tipInitial update of tip values following uppass reconstruction.
N1SprNumber of trees on SPR step away Formula given by Given by...
NamedConstantNamed constant
NewickTreeNewick Tree
NeworderPhyloneworder_phylo Wrapper for the ape function
NeworderPruningwiseneworder_pruningwise Wrapper for the ape function
NJTreeNeighbour Joining Tree
NonDuplicateRootNon-duplicate root
NRootedNumber of rooted/unrooted trees These functions return the...
OrderEdgesNumberNodesOrder edges and number nodes Wrapper for the C function
PhyDat2MorphyInitialize a Morphy Object from a phyDat object
PhyToStringExtract character data from a phyDat object as a string
PrepareDataProfilePrepare data for Profile Parsimony
ProfileScoreProfile Parsimony Score
RandomMorphyTreeRandom postorder tree
RandomTreeGenerate random tree topology from dataset
RandomTreeScoreParsimony score of random postorder tree
RatchetParsimony Ratchet
ReadCharactersRead characters from Nexus file
ReadTntTreeParse TNT Tree
RearrangeEdgesRearrange edges of a phylogenetic tree
referenceTreeTree topology for matrix simulation
RenumberRenumber a tree's nodes and tips
RenumberTipsReorder tips
RenumberTreeRenumber a tree Order edges and number nodes Wrapper for the...
RightmostCharacterRightmost character of string
RootTreeRoot Tree on specified tips
SampleOneQuick sample
SetMorphyWeightsSet the character weightings associated with a Morphy object
SingleCharMorphyMorphy object from single character
SortTreeSort tree
SplitFrequencyFrequency of splits
SplitsRepeatedAre Splits Repeated?
SPRSubtree Pruning and Rearrangement
StringToPhyDatString to phyDat
SuboptimalityTree suboptimality
SubtreeExtract subtree
SuccessiveApproximationsTree Search using Successive Approximations
SuccessiveWeightsSuccessive Weights
summary.morphyPtrDetails the attributes of a morphy object
SupportColourSupport colour
TBRWarningTBR Warning Print a warning and return given tree
TipsAreNamesExtract character data from dataset
TreeSearchSearch for most parsimonious trees
UniqueExceptHitsUnique trees (ignoring 'hits' attribute)
UniqueSplitsUnique Splits
UnloadMorphyDestroy a Morphy Object
UnloadTreeSearchUnload this library
WithOneExtraStepNumber of trees with one extra step
TreeSearch documentation built on Dec. 7, 2018, 5:03 p.m.