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TreeSearch

This package exists to allow parsimony-style tree searches in R.

It extends the basic functionality available in phangorn, with a view to making tree search faster and more efficient, and allowing user-defined optimality criteria to be employed.

Implied weighting and heuristic searches such as the Parsimony Ratchet are implemented (function: Ratchet). Browse the vignettes (with vignette(package = "TreeSearch") to get started.

Installation

Install and load the library from CRAN as follows:

install.packages('TreeSearch')
library('TreeSearch')

If you're feeling brave, you can install the development version thus:

if(!require(devtools)) install.packages("devtools")
devtools::install_github('ms609/TreeSearch')

Optimailty criteria

TreeSearch allows the implementation of various optimality criteria, including

The Profile Parsimony approach introduced by Faith and Trueman (2001).
Successive Approximations weighting (Farris 1969).
Fitch parsimony with inapplicable data (Brazeau, Guillerme and Smith, 2017).

It is also possible to specify bespoke optimality criteria.

References

Brazeau, M. D., Guillerme, T. and Smith, M. R. 2017. Morphological phylogenetic analysis with inapplicable data. BioRχiv. doi:10.1101/209775

D. P. Faith, J. W. H. Trueman, Towards an inclusive philosophy for phylogenetic inference. Syst. Biol. 50, 331–350 (2001). doi:10.1080/10635150118627

Farris, J. S. (1969). A successive approximations approach to character weighting. Systematic Biology, 18(4), 374–385. doi:10.2307/2412182

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Version

Install

install.packages('TreeSearch')

Monthly Downloads

1,977

Version

0.1.2

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/ms609/TreeSearch

Maintainer

Martin R Smith

Last Published

March 19th, 2018

Functions in TreeSearch (0.1.2)

Add a tip to a phylogenetic tree

ConsensusWithout

Consensus without taxa

List all ancestral nodes

Double factorial

Convert a number to binary

Node depth Wrapper for the ape function

Reorder tree Cladewise

EnforceOutgroup

Force taxa to form an outgroup

Extract taxa from a matrix block

Information content per step

DescendantEdges

Descendant Edges

Information Content Steps

Calculate parsimony score with inapplicable data

Edge matrix to edge list

Matrix to phydat

Data from Zhang et al. 2016 in phyDat format

Logistic Points Extract points from a fitted model

Log double factorial Handles odd and even inout numbers

Report the character weightings associated with 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.

Log double factorial

MorphyTreeLength

Calculate parsimony score with inapplicable data

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

Neighbour Joining Tree

Implied weights parsimony Score

Profile Parsimony Score

Amount of information in each character

MorphyErrorCheck

Check for error whilst modifying Morphy object

Rearrange edges of a phylogenetic tree

PrepareDataProfile

Prepare data for Profile Parsimony

Renumber a tree's nodes and tips

Edge list to edge matrix

SuccessiveWeights

Successive Weights

RandomTreeScore

Parsimony score of random postorder tree

RandomMorphyTree

Random postorder tree

Raw data from Zhang et al. 2016

Parsimony Ratchet

Read characters from Nexus file

Generate random tree topology from dataset

MorphyBootstrap

Ratchet bootstrapper

Initialize a Morphy Object from a phyDat object

Brewer palettes

neworder_phylo Wrapper for the ape function

congreveLamsdellMatrices

100 simulated data matrices

Extract character data from a phyDat object as a string

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

Extract subtree

NeworderPruningwise

neworder_pruningwise Wrapper for the ape function

TBR Warning Print a warning and return given tree

NonDuplicateRoot

Non-duplicate root

SuccessiveApproximations

Tree Search using Successive Approximations

Extract character data from dataset

inapplicable.datasets

Thirty Datasets with Inapplicable data

RightmostCharacter

Rightmost character of string

Search for most parsimonious trees

OrderEdgesNumberNodes

Order edges and number nodes Wrapper for the C function

inapplicable.phyData

Thirty Datasets with Inapplicable data

Subtree Pruning and Rearrangement

UnloadTreeSearch

Unload this library

mpl_apply_tipdata

Commits parameters prior to nodal set calculations.

WithOneExtraStep

Number of trees with one extra step

String to phyDat

SingleCharMorphy

Morphy object from single character

mpl_set_num_internal_nodes

Sets the number of internal nodes in the dataset

SingleTaxonTree

SingleTaxonTree

inapplicable.citations

Thirty Datasets with Inapplicable data

Tree suboptimality

mpl_set_parsim_t

Sets a character's parsimony function type

mpl_delete_rawdata

Deletes the caller-input data.

mpl_attach_rawdata

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

Destroy a Morphy Object

mpl_get_num_internal_nodes

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

Initial update of tip values following uppass reconstruction.

mpl_first_down_recon

Reconstructs the first (downpass) nodal reconstructions

mpl_first_up_recon

Reconstructs the second (uppass) nodal reconstructions.

mpl_get_numtaxa

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

Tree topology for matrix simulation

mpl_translate_error

Converts a numeric error code to human-readable format

mpl_get_charac_weight

Retrieve the weight of a character in the dataset

Creates a new instance of a Morphy object

mpl_update_lower_root

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

mpl_get_num_charac

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

mpl_second_down_recon

Performs the second nodal reconstructions for characters with inapplicability.

SetMorphyWeights

Set the character weightings associated with a Morphy object

mpl_get_symbols

Retrieves the current list of symbols.

mpl_delete_Morphy

Destroys an instance of a Morphy object.

mpl_second_up_recon

Finalises the ancestral state reconstructions for characters with inapplicable values.

mpl_init_Morphy

Sets up the dimensions of the dataset.

mpl_attach_symbols

Attach a caller-specified list of symbols.

mpl_set_charac_weight

Set the weight of a character in the dataset

summary.morphyPtr

Details the attributes of a morphy object