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TreeSearch (version 1.0.1)

Phylogenetic Tree Search Using Custom Optimality Criteria

Description

Search for phylogenetic trees that are optimal using a user-defined criterion. Contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees. Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) using the "Morphy" library. Implements Profile Parsimony (Faith and Trueman, 2001) , and Successive Approximations (Farris, 1969) .

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Install

install.packages('TreeSearch')

Monthly Downloads

713

Version

1.0.1

License

GPL (>= 3)

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Repository

https://github.com/ms609/TreeSearch/

Homepage

https://ms609.github.io/TreeSearch/

Maintainer

Martin R. Smith

Last Published

September 27th, 2021

Functions in TreeSearch (1.0.1)

CharacterLength

Character length

Consistency / retention 'indices'

Jackknife resampling

Read how a Morphy Object handles the inapplicable token

ConcordantInformation

Evaluate the concordance of information between a tree and a dataset

Number of trees with m additional steps

Label nodes with jackknife support values

PrepareDataProfile

Prepare data for Profile Parsimony

Nearest neighbour interchange (NNI)

SiteConcordance

Calculate site concordance factor

SingleCharMorphy

Morphy object from single character

Set and get the character weightings associated with a Morphy object.

.CombineResults

Combine two edge matrices

MaximizeParsimony

Find most parsimonious trees

Initialize a Morphy object from a phyDat object

SuccessiveApproximations

Tree search using successive approximations

Tree suboptimality

RandomTreeScore

Parsimony score of random postorder tree

StepInformation

Information content of a character known to contain e steps

Plot the distribution of a character on a tree

StopUnlessBifurcating

Check that all nodes in a tree are bifurcating.

Subtree pruning and rearrangement (SPR)

MorphyTreeLength

Calculate parsimony score from Morphy object

Rearrange edges of a phylogenetic tree

Tree bisection and reconnection (TBR)

WithOneExtraStep

Number of trees with one extra step

Destroy a Morphy object

MorphyErrorCheck

Check for error whilst modifying Morphy object

Is an object a valid Morphy object?

Translate a gap treatment into a string in the format expected by Morphy

mpl_apply_tipdata

Commits parameters prior to nodal set calculations.

RandomMorphyTree

Random postorder tree

inapplicable.phyData

Thirty datasets with inapplicable data

mpl_first_up_recon

Reconstructs the second (uppass) nodal reconstructions.

inapplicable.datasets

Thirty datasets with inapplicable data

mpl_first_down_recon

Reconstructs the first (downpass) nodal reconstructions

mpl_second_down_recon

Performs the second nodal reconstructions for characters with inapplicability.

Calculate the parsimony score of a tree given a dataset

MorphyBootstrap

Parsimony Ratchet

Search for most parsimonious trees

mpl_second_up_recon

Finalises the ancestral state reconstructions for characters with inapplicable values.

cSPR() expects a tree rooted on a single tip.

.UniqueExceptHits

Unique trees (ignoring 'hits' attribute)

inapplicable.citations

Thirty datasets with inapplicable data

mpl_init_Morphy

Sets up the dimensions of the dataset.

mpl_set_parsim_t

Sets a character's parsimony function type

TBR Warning Print a warning and return given tree

mpl_get_charac_weight

Retrieve the weight of a character in the dataset

Creates a new instance of a Morphy object

mpl_translate_error

Converts a numeric error code to human-readable format

mpl_attach_rawdata

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

Empirically counted profiles for small trees

mpl_get_num_charac

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

mpl_get_num_internal_nodes

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

mpl_attach_symbols

Attach a caller-specified list of symbols.

Tree topology for matrix simulation

congreveLamsdellMatrices

100 simulated data matrices

mpl_delete_Morphy

Destroys an instance of a Morphy object.

mpl_get_numtaxa

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

mpl_delete_rawdata

Deletes the caller-input data.

mpl_get_gaphandl

Get / set gap handler from a Morphy object.

mpl_get_symbols

Retrieves the current list of symbols.

mpl_set_num_internal_nodes

Sets the number of internal nodes in the dataset

mpl_set_charac_weight

Set the weight of a character in the dataset

mpl_update_lower_root

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

Initial update of tip values following uppass reconstruction.

summary.morphyPtr

Details the attributes of a morphy object