This package is considered a duplicate. The official version of this package is found at:https://ms609.r-universe.dev/TreeSearch

Package: TreeSearch 1.8.0.9001

Martin R. Smith

TreeSearch: Phylogenetic Analysis with Discrete Character Data

Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> 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) <doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris, 1969) <doi:10.2307/2412182> and custom optimality criteria are implemented.

Authors:Martin R. Smith [aut, cre, cph], Martin Brazeau [cph]

# Install 'TreeSearch' in R:

install.packages('TreeSearch', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ms609/treesearch/issues

Pkgdown/docs site:https://ms609.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

congreveLamsdellMatrices - 100 simulated data matrices
inapplicable.citations - Thirty datasets with inapplicable data
inapplicable.datasets - Thirty datasets with inapplicable data
inapplicable.phyData - Thirty datasets with inapplicable data
inapplicable.trees - Thirty datasets with inapplicable data
profiles - Empirically counted profiles for small trees
referenceTree - Tree topology for matrix simulation

On CRAN:

bioinformatics morphological-analysis phylogenetics research-tool tree-search cpp

6.49 score 9 stars 44 scripts 879 downloads 3 mentions 115 exports 58 dependencies

Last updated from:30bd4ba77a. Checks:12 ERROR, 1 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	ERROR	186
linux-devel-x86_64	ERROR	189
source / vignettes	ERROR	294
linux-release-arm64	ERROR	185
linux-release-x86_64	ERROR	173
macos-release-arm64	ERROR	144
macos-release-x86_64	ERROR	318
macos-oldrel-arm64	ERROR	129
macos-oldrel-x86_64	ERROR	273
windows-devel	ERROR	176
windows-release	ERROR	162
windows-oldrel	ERROR	161
wasm-release	OK	146

Exports:.NonDuplicateRoot .UniqueExceptHits AdditionTree C_MorphyLength Carter1 CharacterLength ClusteringConcordance ClusterStrings cNNI ConcordanceTable ConcordantInfo ConcordantInformation Consistency cSPR DoNothing EasyTrees EasyTreesy EdgeListSearch EmptyPhyDat Evaluate ExpectedLength Fitch FitchSteps GapHandler GetMorphyLength is.morphyPtr IWScore IWTreeSearch Jackknife JackLabels LengthAdded Log2Carter1 LogCarter1 MaximizeParsimony MaximumLength MinimumLength MorphyBootstrap MorphyErrorCheck MorphyLength MorphyTreeLength MorphyWeights MostContradictedFreq mpl_apply_tipdata mpl_attach_rawdata mpl_attach_symbols mpl_delete_Morphy mpl_first_down_recon mpl_first_up_recon mpl_get_charac_weight mpl_get_gaphandl mpl_get_num_charac mpl_get_num_internal_nodes mpl_get_numtaxa mpl_get_symbols mpl_init_Morphy mpl_new_Morphy mpl_second_down_recon mpl_second_up_recon mpl_set_charac_weight mpl_set_gaphandl mpl_set_num_internal_nodes mpl_set_parsim_t mpl_translate_error mpl_update_lower_root mpl_update_tip MultiRatchet MutualClusteringConcordance NNI NNISwap PhyDat2Morphy PhylogeneticConcordance PlotCharacter PolEscapa PrepareDataIW PrepareDataProfile PresCont QACol QALegend QCol QuartetConcordance QuartetResolution RandomMorphyTree RandomTreeScore Ratchet RatchetConsensus RearrangeEdges Resample RootedNNI RootedNNISwap RootedSPR RootedSPRSwap RootedTBR RootedTBRSwap SetMorphyWeights SharedPhylogeneticConcordance SingleCharMorphy SPR SPRMoves SPRSwap SPRWarning StepInformation StopUnlessBifurcating Suboptimality SuccessiveApproximations SuccessiveWeights TaxonInfluence TBR TBRMoves TBRSwap TBRWarning TreeLength TreeSearch UnloadMorphy WhenFirstHit WithOneExtraStep

Dependencies:abind ape base64enc bit bit64 bslib cachem cli cluster codetools colorspace commonmark digest fastmap fastmatch fontawesome fs future globals glue htmltools httpuv jquerylib jsonlite later lattice lifecycle listenv magrittr matrixStats memoise mime nlme otel parallelly PlotTools promises protoclust R6 rappdirs rbibutils Rcpp RcppArmadillo RcppParallel Rdpack Rfast rlang Rogue sass shiny shinyjs sourcetools stringi TreeDist TreeTools withr xtable zigg

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Addition tree	AdditionTree
All SPR trees	AllSPR
Number of trees with _m_ steps	Carter1 Log2Carter1 LogCarter1
Character length	CharacterLength FastCharacterLength
Cluster similar strings	ClusterStrings
Plot concordance table	ConcordanceTable
Evaluate the concordance of information between a tree and a dataset	ConcordantInfo ConcordantInformation Evaluate
100 simulated data matrices	congreveLamsdellMatrices
Consistency and retention "indices"	Consistency
'cSPR()' expects a tree rooted on a single tip.	cSPR
Expected length	ExpectedLength
Read how a Morphy Object handles the inapplicable token	GapHandler
Thirty datasets with inapplicable data	inapplicable.citations inapplicable.datasets inapplicable.phyData inapplicable.trees
Is an object a valid Morphy object?	is.morphyPtr
Calculate the parsimony score of a tree given a dataset	Fitch IWScore TreeLength TreeLength.list TreeLength.multiPhylo TreeLength.numeric TreeLength.phylo
Jackknife resampling	Jackknife
Label nodes with jackknife support values	JackLabels
Contribution of character to leaf instability	LengthAdded PolEscapa
Find most parsimonious trees	EasyTrees EasyTreesy MaximizeParsimony Resample
Minimum and Maximum lengths possible for a character	MaximumLength MaximumLength.character MaximumLength.numeric MinimumLength MinimumLength.character MinimumLength.numeric MinimumLength.phyDat MinimumSteps
Parsimony Ratchet	MorphyBootstrap MultiRatchet Ratchet RatchetConsensus
Set and get the character weightings associated with a Morphy object.	MorphyWeights SetMorphyWeights
Frequency of most common contradictory split	MostContradictedFreq
Nearest neighbour interchange (NNI)	cNNI NNI NNISwap RootedNNI RootedNNISwap
Initialize a Morphy object from a 'phyDat' object	PhyDat2Morphy
Plot the distribution of a character on a tree	PlotCharacter PlotCharacter.list PlotCharacter.multiPhylo PlotCharacter.phylo
Prepare data for Profile Parsimony	PrepareDataIW PrepareDataProfile
Group present or contradicted score	PresCont
Empirically counted profiles for small trees	profiles
Generate colour to depict the amount and quality of observations	QACol QALegend QCol
Relationship between four taxa	QuartetResolution
Random postorder tree	RandomMorphyTree
Parsimony score of random postorder tree	RandomTreeScore
Rearrange edges of a phylogenetic tree	RearrangeEdges
Tree topology for matrix simulation	referenceTree
Morphy object from single character	SingleCharMorphy
Concordance factors	ClusteringConcordance MutualClusteringConcordance PhylogeneticConcordance QuartetConcordance SharedPhylogeneticConcordance SiteConcordance
Subtree pruning and rearrangement (SPR)	RootedSPR RootedSPRSwap SPR SPRMoves SPRMoves.matrix SPRMoves.phylo SPRSwap
Information content of a character known to contain _e_ steps	StepInformation
Details the attributes of a morphy object	summary.morphyPtr
Rank taxa by their influence on phylogenetic results	TaxonInfluence
Tree bisection and reconnection (TBR)	RootedTBR RootedTBRSwap TBR TBRMoves TBRMoves.matrix TBRMoves.phylo TBRSwap
Destroy a Morphy object	UnloadMorphy
When was a tree topology first hit?	WhenFirstHit
Number of trees with one extra step	WithOneExtraStep

Package: TreeSearch 1.8.0.9001

TreeSearch: Phylogenetic Analysis with Discrete Character Data

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