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TreeSearch (version 0.3.2)

Phylogenetic Tree Search Using Custom Optimality Criteria

Description

Searches for phylogenetic trees that are optimal using a user-defined criterion. Implements Profile Parsimony (Faith and Trueman, 2001) , and Successive Approximations (Farris, 1969) . Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) .

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Install

install.packages('TreeSearch')

Monthly Downloads

702

Version

0.3.2

License

GPL (>= 3)

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Repository

https://github.com/ms609/TreeSearch

Maintainer

Martin R. Smith

Last Published

June 3rd, 2019

Functions in TreeSearch (0.3.2)

EnforceOutgroup

Force taxa to form an outgroup

DropSingleSplits

Drop Single Splits

Convert a number to binary

Node depth Wrapper for the ape function

Entropy in bits

Information content per step

Raw data from Zhang et al. 2016

Number of rooted/unrooted trees These functions return the number of rooted or unrooted trees consistent with a given pattern of splits.

Data from Zhang et al. 2016 in phyDat format

Calculate parsimony score with inapplicable data

OrderEdgesNumberNodes

Order edges and number nodes Wrapper for the C function

Initialize a Morphy Object from a phyDat object

Root Tree on specified tips

Implied weights parsimony Score

DoubleFactorial

Double Factorial

Amount of information in each character

Subtree Pruning and Rearrangement (SPR)

SplitMutualInformation

Mutual information of two splits

SplitMatchProbability

Probability of matching this well

Information Content Steps

Edge matrix to edge list

Matrix to phydat

MorphyErrorCheck

Check for error whilst modifying Morphy object

MorphyTreeLength

Calculate parsimony score with inapplicable data

Report the character weightings associated with a Morphy object

MutualArborealInfo

Information-based generalized Robinson-Foulds distance between two trees

Profile Parsimony Score

Tree bisection and reconnection (TBR)

RandomMorphyTree

Random postorder tree

Renumber a tree's nodes and tips

NonDuplicateRoot

Non-duplicate root

neworder_phylo Wrapper for the ape function

NyeTreeSimilarity

Nye et al. (2006) tree comparison

NeworderPruningwise

neworder_pruningwise Wrapper for the ape function

Parsimony Ratchet

Search for most parsimonious trees

Frequency of splits

SplitInformation

Information content of a split

Are Splits Repeated?

SplitsCompatible

Are splits compatible?

Read characters from Nexus file

Entropy of two splits

SuccessiveApproximations

Tree Search using Successive Approximations

CalculateTreeDistance

Wrapper for tree distance calculations

Collapse nodes on a phylogenetic tree

Extract taxa from a matrix block

Reorder tree Cladewise

SuccessiveWeights

Successive Weights

logDoubleFactorials

Natural logarithms of double factorials

TBR Warning Print a warning and return given tree

TreesMatchingSplit

Number of trees matching a bipartition split

UniqueExceptHits

Unique trees (ignoring 'hits' attribute)

mpl_get_numtaxa

Retrieve the number of taxa (rows) in the dataset.

inapplicable.datasets

Thirty Datasets with Inapplicable data

inapplicable.phyData

Thirty Datasets with Inapplicable data

mpl_get_num_internal_nodes

Gets the number of internal nodal reconstruction sets being used by MorphyLib.

mpl_apply_tipdata

Commits parameters prior to nodal set calculations.

Extract character data from dataset

AllSplitPairings

All split pairings

mpl_init_Morphy

Sets up the dimensions of the dataset.

mpl_get_symbols

Retrieves the current list of symbols.

mpl_attach_symbols

Attach a caller-specified list of symbols.

JointInformation

Joint Information of two splits

mpl_attach_rawdata

Attach raw character state data (i.e. tip data).

Edge list to edge matrix

Logistic Points Extract points from a fitted model

ConsensusWithout

Consensus without taxa

DescendantEdges

Descendant Edges

mpl_set_num_internal_nodes

Sets the number of internal nodes in the dataset

MorphyBootstrap

Ratchet bootstrapper

Generate random tree topology from dataset

Neighbour Joining Tree

Number of trees one SPR step away Formula given by Allen and Steel (2001).

RandomTreeScore

Parsimony score of random postorder tree

SingleCharMorphy

Morphy object from single character

SingleTaxonTree

SingleTaxonTree

Rearrange edges of a phylogenetic tree

mpl_set_parsim_t

Sets a character's parsimony function type

summary.morphyPtr

Details the attributes of a morphy object

MatchingSplitDistance

Matching Split Distance

Nearest Neighbour Interchange (NNI)

String to phyDat

StopUnlessBifurcating

Check that all nodes in a tree are bifurcating.

NPartitionPairs

Distributions of taxa consistent with a partition pair.

mpl_translate_error

Converts a numeric error code to human-readable format

mpl_get_num_charac

Retrieve the number of character (columns) in the dataset.

mpl_get_charac_weight

Retrieve the weight of a character in the dataset

inapplicable.citations

Thirty Datasets with Inapplicable data

doubleFactorials

Double factorials

Extract character data from a phyDat object as a string

mpl_update_lower_root

Updates the nodal sets for a lower ('dummy') root node

Destroy a Morphy Object

mpl_first_down_recon

Reconstructs the first (downpass) nodal reconstructions

WithOneExtraStep

Number of trees with one extra step

VisualizeMatching

Visualise a matching

mpl_second_down_recon

Performs the second nodal reconstructions for characters with inapplicability.

mpl_first_up_recon

Reconstructs the second (uppass) nodal reconstructions.

Creates a new instance of a Morphy object

Renumber a tree Order edges and number nodes Wrapper for the C function RENUMBER_TREE

PrepareDataProfile

Prepare data for Profile Parsimony

RightmostCharacter

Rightmost character of string

SetMorphyWeights

Set the character weightings associated with a Morphy object

UnloadTreeSearch

Unload this library

Brewer palettes

UnrootedTreesMatchingSplit

Number of trees consistent with split

Extract subtree

congreveLamsdellMatrices

100 simulated data matrices

Tree suboptimality

mpl_delete_Morphy

Destroys an instance of a Morphy object.

mpl_delete_rawdata

Deletes the caller-input data.

mpl_second_up_recon

Finalises the ancestral state reconstructions for characters with inapplicable values.

mpl_set_charac_weight

Set the weight of a character in the dataset

Initial update of tip values following uppass reconstruction.

Tree topology for matrix simulation

Add a tip to a phylogenetic tree

List all ancestral nodes