Package: TreeSearch 1.5.1
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:
TreeSearch_1.5.1.tar.gz
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TreeSearch.pdf |TreeSearch.html✨
TreeSearch/json (API)
NEWS
# 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
- 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
bioinformaticsmorphological-analysisphylogeneticsresearch-tooltree-search
Last updated 3 days agofrom:3bd6fab8e1. Checks:OK: 7 NOTE: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Sep 05 2024 |
R-4.5-win-x86_64 | NOTE | Sep 05 2024 |
R-4.5-linux-x86_64 | NOTE | Sep 05 2024 |
R-4.4-win-x86_64 | OK | Sep 05 2024 |
R-4.4-mac-x86_64 | OK | Sep 05 2024 |
R-4.4-mac-aarch64 | OK | Sep 05 2024 |
R-4.3-win-x86_64 | OK | Sep 05 2024 |
R-4.3-mac-x86_64 | OK | Sep 05 2024 |
R-4.3-mac-aarch64 | OK | Sep 05 2024 |
Exports:.NonDuplicateRoot.UniqueExceptHitsAdditionTreeC_MorphyLengthCarter1CharacterLengthClusteringConcordanceClusterStringscNNIConcordantInfoConcordantInformationConsistencycSPRDoNothingEasyTreesEasyTreesyEdgeListSearchEmptyPhyDatEvaluateFitchFitchStepsGapHandlerGetMorphyLengthis.morphyPtrIWScoreIWTreeSearchJackknifeJackLabelsLengthAddedLog2Carter1LogCarter1MaximizeParsimonyMaximumLengthMinimumLengthMorphyBootstrapMorphyErrorCheckMorphyLengthMorphyTreeLengthMorphyWeightsmpl_apply_tipdatampl_attach_rawdatampl_attach_symbolsmpl_delete_Morphympl_delete_rawdatampl_first_down_reconmpl_first_up_reconmpl_get_charac_weightmpl_get_gaphandlmpl_get_num_characmpl_get_num_internal_nodesmpl_get_numtaxampl_get_symbolsmpl_init_Morphympl_new_Morphympl_second_down_reconmpl_second_up_reconmpl_set_charac_weightmpl_set_gaphandlmpl_set_num_internal_nodesmpl_set_parsim_tmpl_translate_errormpl_update_lower_rootmpl_update_tipMultiRatchetMutualClusteringConcordanceNNINNISwapPhyDat2MorphyPhylogeneticConcordancePlotCharacterPolEscapaPrepareDataIWPrepareDataProfileQuartetConcordanceQuartetResolutionRandomMorphyTreeRandomTreeScoreRatchetRatchetConsensusRearrangeEdgesResampleRootedNNIRootedNNISwapRootedSPRRootedSPRSwapRootedTBRRootedTBRSwapSetMorphyWeightsSharedPhylogeneticConcordanceSingleCharMorphySPRSPRMovesSPRSwapSPRWarningStepInformationStopUnlessBifurcatingSuboptimalitySuccessiveApproximationsSuccessiveWeightsTaxonInfluenceTBRTBRMovesTBRSwapTBRWarningTreeLengthTreeSearchUnloadMorphyWhenFirstHitWithOneExtraStep
Dependencies:apebase64encbitbit64bitopsbslibcachemcliclustercodetoolscolorspacecommonmarkcrayondigestfastmapfastmatchfontawesomefsfutureglobalsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclelistenvmagrittrmatrixStatsmemoisemimenlmeparallellyPlotToolspromisesprotoclustR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratRCurlRdpackRfastrlangRoguesassshinyshinyjssourcetoolsTreeDistTreeToolswithrxtable
Getting started: Exploring tree space
Rendered fromtree-space.Rmd
usingknitr::rmarkdown
on Sep 05 2024.Last update: 2023-07-17
Started: 2022-08-15
Getting started: Installing R and TreeSearch
Rendered fromgetting-started.Rmd
usingknitr::rmarkdown
on Sep 05 2024.Last update: 2023-07-17
Started: 2018-02-21
Getting started: Simple tree searches
Rendered fromtree-search.Rmd
usingknitr::rmarkdown
on Sep 05 2024.Last update: 2023-07-17
Started: 2021-05-14
Profile parsimony
Rendered fromprofile-scores.Rmd
usingknitr::rmarkdown
on Sep 05 2024.Last update: 2023-07-17
Started: 2018-02-21
Tree search with custom optimality criteria
Rendered fromcustom.Rmd
usingknitr::rmarkdown
on Sep 05 2024.Last update: 2023-07-17
Started: 2021-04-14
Tree search with Profile parsimony
Rendered fromprofile.Rmd
usingknitr::rmarkdown
on Sep 05 2024.Last update: 2023-08-26
Started: 2018-02-21