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TreeSearch (version 1.1.0)

Phylogenetic Analysis with Morphological Data

Description

Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) with the "Morphy" library, under equal or implied step weights. 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 (Smith 2022a, b) , . Profile Parsimony (Faith and Trueman, 2001) , Successive Approximations (Farris, 1969) and custom optimality criteria are implemented.

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Install

install.packages('TreeSearch')

Monthly Downloads

713

Version

1.1.0

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

January 17th, 2022

Functions in TreeSearch (1.1.0)

Read how a Morphy Object handles the inapplicable token

Number of trees with m steps

Nearest neighbour interchange (NNI)

CharacterLength

Character length

Initialize a Morphy object from a phyDat object

MaximizeParsimony

Find most parsimonious trees

Jackknife resampling

Consistency / retention 'indices'

Subtree pruning and rearrangement (SPR)

Plot the distribution of a character on a tree

PrepareDataProfile

Prepare data for Profile Parsimony

SingleCharMorphy

Morphy object from single character

StepInformation

Information content of a character known to contain e steps

Search for most parsimonious trees

SiteConcordance

Calculate site concordance factor

Label nodes with jackknife support values

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

Cluster similar strings

ConcordantInformation

Evaluate the concordance of information between a tree and a dataset

StopUnlessBifurcating

Check that all nodes in a tree are bifurcating.

MorphyBootstrap

Parsimony Ratchet

SuccessiveApproximations

Tree search using successive approximations

Tree suboptimality

MorphyTreeLength

Calculate parsimony score from Morphy object

MorphyErrorCheck

Check for error whilst modifying Morphy object

Rearrange edges of a phylogenetic tree

mpl_attach_rawdata

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

mpl_apply_tipdata

Commits parameters prior to nodal set calculations.

mpl_get_charac_weight

Retrieve the weight of a character in the dataset

mpl_first_up_recon

Reconstructs the second (uppass) nodal reconstructions.

TBR Warning Print a warning and return given tree

Calculate the parsimony score of a tree given a dataset

mpl_get_numtaxa

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

mpl_get_num_internal_nodes

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

mpl_update_lower_root

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

mpl_translate_error

Converts a numeric error code to human-readable format

Destroy a Morphy object

.UniqueExceptHits

Unique trees (ignoring 'hits' attribute)

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

mpl_get_gaphandl

Get / set gap handler from a Morphy object.

Tree bisection and reconnection (TBR)

mpl_attach_symbols

Attach a caller-specified list of symbols.

mpl_delete_Morphy

Destroys an instance of a Morphy object.

RandomMorphyTree

Random postorder tree

mpl_get_num_charac

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

WithOneExtraStep

Number of trees with one extra step

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

RandomTreeScore

Parsimony score of random postorder tree

congreveLamsdellMatrices

100 simulated data matrices

.CombineResults

Combine two edge matrices

Is an object a valid Morphy object?

mpl_second_down_recon

Performs the second nodal reconstructions for characters with inapplicability.

Creates a new instance of a Morphy object

inapplicable.datasets

Thirty datasets with inapplicable data

mpl_second_up_recon

Finalises the ancestral state reconstructions for characters with inapplicable values.

mpl_delete_rawdata

Deletes the caller-input data.

mpl_first_down_recon

Reconstructs the first (downpass) nodal reconstructions

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

mpl_set_charac_weight

Set the weight of a character in the dataset

summary.morphyPtr

Details the attributes of a morphy object

Tree topology for matrix simulation

mpl_get_symbols

Retrieves the current list of symbols.

Initial update of tip values following uppass reconstruction.

mpl_init_Morphy

Sets up the dimensions of the dataset.

Empirically counted profiles for small trees