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TreeSearch (version 0.2.2)

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

0.2.2

License

GPL (>= 3)

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Repository

https://github.com/ms609/TreeSearch

Maintainer

Martin R. Smith

Last Published

January 2nd, 2019

Functions in TreeSearch (0.2.2)

Add a tip to a phylogenetic tree

Logistic Points Extract points from a fitted model

List all ancestral nodes

PrepareDataProfile

Prepare data for Profile Parsimony

Edge matrix to edge list

NeworderPruningwise

neworder_pruningwise Wrapper for the ape function

Information content per step

neworder_phylo Wrapper for the ape function

Profile Parsimony Score

Convert a number to binary

Subtree Pruning and Rearrangement

EnforceOutgroup

Force taxa to form an outgroup

ConsensusWithout

Consensus without taxa

Reorder tree Cladewise

Double factorial

Collapse nodes on a phylogenetic tree

Raw data from Zhang et al. 2016

DropSingleSplits

Drop Single Splits

Extract subtree

SuccessiveApproximations

Tree Search using Successive Approximations

Brewer palettes

SetMorphyWeights

Set the character weightings associated with a Morphy object

SingleCharMorphy

Morphy object from single character

OrderEdgesNumberNodes

Order edges and number nodes Wrapper for the C function

Matrix to phydat

NonDuplicateRoot

Non-duplicate root

Log double factorial

inapplicable.citations

Thirty Datasets with Inapplicable data

inapplicable.datasets

Thirty Datasets with Inapplicable data

congreveLamsdellMatrices

100 simulated data matrices

mpl_init_Morphy

Sets up the dimensions of the dataset.

mpl_get_symbols

Retrieves the current list of symbols.

Edge list to edge matrix

TBR Warning Print a warning and return given tree

Number of trees on SPR step away Formula given by Given by Allen and Steel 2001.

Neighbour Joining Tree

Search for most parsimonious trees

RandomTreeScore

Parsimony score of random postorder tree

Parsimony Ratchet

Data from Zhang et al. 2016 in phyDat format

MorphyTreeLength

Calculate parsimony score with inapplicable data

UniqueExceptHits

Unique trees (ignoring 'hits' attribute)

SingleTaxonTree

SingleTaxonTree

Frequency of splits

Node depth Wrapper for the ape function

Report the character weightings associated with a Morphy object

Are Splits Repeated?

mpl_first_down_recon

Reconstructs the first (downpass) nodal reconstructions

mpl_first_up_recon

Reconstructs the second (uppass) nodal reconstructions.

Creates a new instance of a Morphy object

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

Rearrange edges of a phylogenetic tree

mpl_second_down_recon

Performs the second nodal reconstructions for characters with inapplicability.

Initial update of tip values following uppass reconstruction.

Renumber a tree's nodes and tips

Destroy a Morphy Object

Tree topology for matrix simulation

RightmostCharacter

Rightmost character of string

Extract taxa from a matrix block

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

Root Tree on specified tips

String to phyDat

Calculate parsimony score with inapplicable data

Tree suboptimality

Amount of information in each character

Log double factorial Handles odd and even inout numbers

MorphyBootstrap

Ratchet bootstrapper

MorphyErrorCheck

Check for error whilst modifying Morphy object

RandomMorphyTree

Random postorder tree

Generate random tree topology from dataset

SuccessiveWeights

Successive Weights

UnloadTreeSearch

Unload this library

WithOneExtraStep

Number of trees with one extra step

DescendantEdges

Descendant Edges

mpl_attach_rawdata

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

mpl_delete_Morphy

Destroys an instance of a Morphy object.

mpl_delete_rawdata

Deletes the caller-input data.

Information Content Steps

mpl_attach_symbols

Attach a caller-specified list of symbols.

mpl_get_num_internal_nodes

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

mpl_get_numtaxa

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

mpl_get_charac_weight

Retrieve the weight of a character in the dataset

mpl_get_num_charac

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

Implied weights parsimony Score

Initialize a Morphy Object from a phyDat object

summary.morphyPtr

Details the attributes of a morphy object

mpl_translate_error

Converts a numeric error code to human-readable format

mpl_update_lower_root

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

Extract character data from a phyDat object as a string

Read characters from Nexus file

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

Extract character data from dataset

inapplicable.phyData

Thirty Datasets with Inapplicable data

mpl_apply_tipdata

Commits parameters prior to nodal set calculations.

mpl_set_num_internal_nodes

Sets the number of internal nodes in the dataset

mpl_set_parsim_t

Sets a character's parsimony function type