TreeSearch v0.4.0

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Phylogenetic Tree Search Using Custom Optimality Criteria

Searches for phylogenetic trees that are optimal using a user-defined criterion. Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>. Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.

Functions in TreeSearch

Name Description
Evaluate Evaluate tree
Fitch Calculate parsimony score with inapplicable data
PrepareDataProfile Prepare data for Profile Parsimony
PhyDat2Morphy Initialize a Morphy Object from a phyDat object
RearrangeEdges Rearrange edges of a phylogenetic tree
MorphyErrorCheck Check for error whilst modifying Morphy object
SPR Subtree Pruning and Rearrangement (SPR)
SuccessiveApproximations Tree Search using Successive Approximations
SuccessiveWeights Successive Weights
AllSPR All SPR trees
MorphyTreeLength Calculate parsimony score with inapplicable data
StopUnlessBifurcating Check that all nodes in a tree are bifurcating.
inapplicable.phyData Thirty Datasets with Inapplicable data
mpl_delete_rawdata Deletes the caller-input data.
SingleCharMorphy Morphy object from single character
NNI Nearest Neighbour Interchange (NNI)
mpl_delete_Morphy Destroys an instance of a Morphy object.
ICSteps Information Content Steps
CharacterLength Character length
TBR Tree bisection and reconnection (TBR)
mpl_second_up_recon Finalises the ancestral state reconstructions for characters with inapplicable values.
Suboptimality Tree suboptimality
AsBinary Convert a number to binary
MorphyBootstrap Ratchet bootstrapper
SetMorphyWeights Set the character weightings associated with a Morphy object
mpl_update_tip Initial update of tip values following uppass reconstruction.
SPRWarning TBR Warning Print a warning and return given tree
mpl_attach_rawdata Attach raw character state data (i.e. tip data).
mpl_new_Morphy Creates a new instance of a Morphy object
mpl_apply_tipdata Commits parameters prior to nodal set calculations.
MinimumLength Minimum length
DoubleNNI Double NNI
MorphyWeights Report the character weightings associated with a Morphy object
TipsAreNames Extract character data from dataset
mpl_set_charac_weight Set the weight of a character in the dataset
referenceTree Tree topology for matrix simulation
RandomTreeScore Parsimony score of random postorder tree
mpl_second_down_recon Performs the second nodal reconstructions for characters with inapplicability.
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
JackLabels Label nodes with jackknife support values
ICS Information content per step
WithOneExtraStep Number of trees with one extra step
IWTreeSearch Search for most parsimonious trees
mpl_get_num_charac Retrieve the number of character (columns) in the dataset.
Jackknife Parsimony Ratchet
IWScoreMorphy Profile Parsimony Score
mpl_attach_symbols Attach a caller-specified list of symbols.
mpl_get_symbols Retrieves the current list of symbols.
mpl_first_down_recon Reconstructs the first (downpass) nodal reconstructions
mpl_init_Morphy Sets up the dimensions of the dataset.
UniqueExceptHits Unique trees (ignoring 'hits' attribute)
congreveLamsdellMatrices 100 simulated data matrices
LogisticPoints Logistic Points Extract points from a fitted model
RandomMorphyTree Random postorder tree
mpl_first_up_recon Reconstructs the second (uppass) nodal reconstructions.
UnloadMorphy Destroy a Morphy Object
mpl_get_charac_weight Retrieve the weight of a character in the dataset
mpl_get_numtaxa Retrieve the number of taxa (rows) in the dataset.
inapplicable.citations Thirty Datasets with Inapplicable data
mpl_set_num_internal_nodes Sets the number of internal nodes in the dataset
mpl_get_num_internal_nodes Gets the number of internal nodal reconstruction sets being used by MorphyLib.
inapplicable.datasets Thirty Datasets with Inapplicable data
summary.morphyPtr Details the attributes of a morphy object
mpl_set_parsim_t Sets a character's parsimony function type
IWScore Implied weights parsimony Score
InfoAmounts Amount of information in each character
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Vignettes of TreeSearch

Name
getting-started.Rmd
inapplicable.Rmd
profile-scores.Rmd
profile.Rmd
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Details

License GPL (>= 3)
Copyright Incorporates C/C++ code from Morphy Phylogenetic Library by Martin Brazeau (GPL3)
URL https://ms609.github.io/TreeSearch, https://github.com/ms609/TreeSearch
BugReports https://github.com/ms609/TreeSearch/issues
RdMacros Rdpack
LazyData true
ByteCompile true
Encoding UTF-8
Language en-GB
VignetteBuilder knitr
RoxygenNote 6.1.1
NeedsCompilation yes
Packaged 2020-02-06 10:48:09 UTC; ms609
Repository CRAN
Date/Publication 2020-02-06 11:30:06 UTC

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