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TreeSearch
View on CRAN: Click
here
Download and install TreeSearch package within the R console
Install from CRAN:
install.packages("TreeSearch")
Install from Github:
library("remotes")
install_github("cran/TreeSearch")
Install by package version:
library("remotes")
install_version("TreeSearch", "1.5.0")
Attach the package and use:
library("TreeSearch")
Maintained by
Martin R. Smith
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-11-07
Latest Update: 2023-08-26
Description:
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.
How to cite:
Martin R. Smith (2017). TreeSearch: Phylogenetic Analysis with Discrete Character Data. R package version 1.5.0, https://cran.r-project.org/web/packages/TreeSearch
Previous versions and publish date:
0.0.6 (2017-11-07 14:01), 0.0.8 (2018-03-08 23:47), 0.1.0 (2018-03-14 16:40), 0.1.2 (2018-03-19 20:18), 0.2.0 (2018-09-11 13:00), 0.2.1 (2018-12-07 12:20), 0.2.2 (2019-01-02 14:30), 0.3.0 (2019-03-21 10:03), 0.3.2 (2019-06-03 17:30), 0.4.0 (2020-02-06 12:30), 0.4.1 (2020-06-09 10:30), 0.4.2 (2020-07-07 13:00), 0.4.3 (2020-07-09 14:20), 1.0.0 (2021-09-22 12:10), 1.0.1 (2021-09-27 16:10), 1.1.0 (2022-01-17 18:12), 1.1.1 (2022-03-22 11:10), 1.1.2 (2022-05-11 13:20), 1.2.0 (2022-08-11 00:40), 1.3.0 (2023-02-20 10:40), 1.3.1 (2023-03-29 14:30), 1.3.2 (2023-04-27 14:52), 1.4.0 (2023-08-26 06:50)
Other packages that cited TreeSearch R package
View TreeSearch citation profile
Other R packages that TreeSearch depends,
imports, suggests or enhances
Functions, R codes and Examples using
the TreeSearch R package
Some associated functions: AdditionTree . AllSPR . Carter1 . CharacterLength . ClusterStrings . ConcordantInformation . Consistency . DoubleNNI . GapHandler . JackLabels . Jackknife . MaximizeParsimony . MinimumLength . MorphyErrorCheck . MorphyTreeLength . MorphyWeights . NNI . PhyDat2Morphy . PlotCharacter . PrepareDataProfile . QuartetResolution . RandomMorphyTree . RandomTreeScore . Ratchet . RearrangeEdges . SPR . SingleCharMorphy . SiteConcordance . StepInformation . StopUnlessBifurcating . Suboptimality . SuccessiveApproximations . TBR . TBRWarning . TreeLength . TreeSearch . UnloadMorphy . WithOneExtraStep . cSPR . congreveLamsdellMatrices . dot-CombineResults . dot-GapHandler . dot-NonDuplicateRoot . dot-UniqueExceptHits . inapplicable.datasets . is.morphyPtr . mpl_apply_tipdata . mpl_attach_rawdata . mpl_attach_symbols . mpl_delete_Morphy . mpl_delete_rawdata . 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_num_internal_nodes . mpl_set_parsim_t . mpl_translate_error . mpl_update_lower_root . mpl_update_tip . profiles . referenceTree . summary.morphyPtr .
Some associated R codes: AdditionTree.R . Bootstrap.R . ClusterStrings.R . Concordance.R . CustomSearch.R . IWScore.R . ImposeConstraint.R . Jackknife.R . MaximizeParsimony.R . NNI.R . PlotCharacter.R . QuartetResolution.R . RandomTreeScore.R . Ratchet.R . RcppExports.R . ReleaseQuestions.R . SPR.R . Sectorial.R . SuccessiveApproximations.R . TBR.R . TreeSearch_utilities.R . ci-ri.R . data.R . data_manipulation.R . length_range.R . mpl_morphy_objects.R . mpl_morphyex.R . mpl_visualise.R . tree_length.R . tree_rearrangement.R . zzz.R . Full TreeSearch package functions and examples
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