Learn R Programming

⚠️There's a newer version (1.6.1) of this package.Take me there.

TreeSearch (version 1.5.0)

Phylogenetic Analysis with Discrete Character 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.

Copy Link

Version

Install

install.packages('TreeSearch')

Monthly Downloads

713

Version

1.5.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/ms609/TreeSearch/ (devel)

Homepage

https://ms609.github.io/TreeSearch/ (doc)

Maintainer

Martin R. Smith

Last Published

April 3rd, 2024

Functions in TreeSearch (1.5.0)

Plot the distribution of a character on a tree

RandomMorphyTree

Random postorder tree

PrepareDataProfile

Prepare data for Profile Parsimony

Calculate the parsimony score of a tree given a dataset

SiteConcordance

Calculate site concordance factor

StepInformation

Information content of a character known to contain e steps

When was a tree topology first hit?

Search for most parsimonious trees

RandomTreeScore

Parsimony score of random postorder tree

Rearrange edges of a phylogenetic tree

Contribution of character to leaf instability

Destroy a Morphy object

MorphyBootstrap

Parsimony Ratchet

.UniqueExceptHits

Unique trees (ignoring "hits" attribute)

congreveLamsdellMatrices

100 simulated data matrices

inapplicable.datasets

Thirty datasets with inapplicable data

.CombineResults

Combine two edge matrices

SuccessiveApproximations

Tree search using successive approximations

TBR Warning Print a warning and return given tree

QuartetResolution

Relationship between four taxa

mpl_attach_symbols

Attach a caller-specified list of symbols.

mpl_attach_rawdata

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

mpl_get_numtaxa

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

mpl_get_symbols

Retrieves the current list of symbols.

Rank taxa by their influence on phylogenetic results

mpl_get_num_charac

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

mpl_set_charac_weight

Set the weight of a character in the dataset

Initial update of tip values following uppass reconstruction.

mpl_set_parsim_t

Sets a character's parsimony function type

mpl_translate_error

Converts a numeric error code to human-readable format

SingleCharMorphy

Morphy object from single character

Subtree pruning and rearrangement (SPR)

mpl_get_num_internal_nodes

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

mpl_set_num_internal_nodes

Sets the number of internal nodes in the dataset

StopUnlessBifurcating

Check that all nodes in a tree are bifurcating.

Tree bisection and reconnection (TBR)

WithOneExtraStep

Number of trees with one extra step

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

mpl_update_lower_root

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

Tree suboptimality

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

.NonDuplicateRoot

Non-duplicate root

mpl_first_up_recon

Reconstructs the second (uppass) nodal reconstructions.

Is an object a valid Morphy object?

summary.morphyPtr

Details the attributes of a morphy object

mpl_second_up_recon

Finalises the ancestral state reconstructions for characters with inapplicable values.

mpl_first_down_recon

Reconstructs the first (downpass) nodal reconstructions

mpl_second_down_recon

Performs the second nodal reconstructions for characters with inapplicability.

mpl_apply_tipdata

Commits parameters prior to nodal set calculations.

mpl_delete_Morphy

Destroys an instance of a Morphy object.

mpl_init_Morphy

Sets up the dimensions of the dataset.

Creates a new instance of a Morphy object

mpl_delete_rawdata

Deletes the caller-input data.

Tree topology for matrix simulation

Empirically counted profiles for small trees

mpl_get_charac_weight

Retrieve the weight of a character in the dataset

mpl_get_gaphandl

Get / set gap handler from a Morphy object.

Cluster similar strings

Read how a Morphy Object handles the inapplicable token

CharacterLength

Character length

Label nodes with jackknife support values

Consistency / retention "indices"

ConcordantInformation

Evaluate the concordance of information between a tree and a dataset

Number of trees with m steps

Initialize a Morphy object from a phyDat object

Jackknife resampling

MorphyErrorCheck

Check for error whilst modifying Morphy object

MaximizeParsimony

Find most parsimonious trees

Nearest neighbour interchange (NNI)

Minimum and Maximum lengths possible for a character

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

MorphyTreeLength

Calculate parsimony score from Morphy object