Files in ms609/TreeSearch
Phylogenetic Tree Search Using Custom Optimality Criteria

.Rbuildignore
.gitattributes
.gitignore
.travis.yml
CONTRIBUTING
DESCRIPTION
NAMESPACE
NEWS.md R/Bootstrap.R R/Fitch.R R/IWScore.R R/Jackknife.R R/NNI.R R/Partitions.R R/RandomTreeScore.R R/Ratchet.R R/RcppExports.R R/ReleaseQuestions.R R/SPR.R R/Sectorial.R R/SuccessiveApproximations.R R/Support.R R/TBR.R R/TreeSearch.R R/ape_interface.R R/data.R R/helper_functions.R R/mpl_morphy_objects.R R/mpl_morphyex.R R/mpl_prepare_data.R R/mpl_visualise.R R/parse_files.R R/phylo.R R/pp_ProfileScore.R R/pp_data_manipulation.R R/pp_info_extra_step.r R/tree_display.R R/tree_generation.R R/tree_numbering.R R/tree_rearrangement.R R/zzz.R README.md
TreeSearch.Rproj
cran-comments.md
data-raw/Agnarsson2004.nex
data-raw/Aguado2009.nex
data-raw/Aria2015.nex
data-raw/Asher2005.nex
data-raw/Capa2011.nex
data-raw/Conrad2008.nex
data-raw/DeAssis2011.nex
data-raw/Dikow2009.nex
data-raw/Eklund2004.nex
data-raw/Geisler2001.nex
data-raw/Giles2015.nex
data-raw/Griswold1999.nex
data-raw/Liljeblad2008.nex
data-raw/Loconte1991.nex
data-raw/Longrich2010.nex
data-raw/Longrich2010.xlsx
data-raw/OLeary1999.nex
data-raw/OMeara2014.nex
data-raw/Rougier2012.nex
data-raw/Rousset2004.nex
data-raw/Sano2011.nex
data-raw/Sansom2010.nex
data-raw/Schulze2007.nex
data-raw/Shultz2007.nex
data-raw/Vinther2008.nex
data-raw/Wetterer2000.nex
data-raw/Wills2012.nex
data-raw/Wilson2003.nex
data-raw/Wortley2006.nex
data-raw/Zanol2014.nex
data-raw/Zhu2013.nex
data-raw/_data_generator.R
data/Lobo.RData
data/brewer.R
data/congreveLamsdellMatrices.RData
data/inapplicable.citations.R
data/inapplicable.datasets.rda
data/inapplicable.phyData.rda
data/referenceTree.RData
inst/CITATION
inst/REFERENCES.bib
inst/apa-old-doi-prefix.csl
inst/tests/benchmark_timing.R man-roxygen/CleanUpDataParam.R man-roxygen/EdgeSwapperParam.R man-roxygen/InitializeDataParam.R man-roxygen/LoboMods.r man-roxygen/characterNumParam.R man-roxygen/clusterParam.R man-roxygen/concavityParam.R man-roxygen/dataForFunction.R man-roxygen/datasetParam.r man-roxygen/edgeListParam.R man-roxygen/edgeToBreakParam.R man-roxygen/inapplicableSources.R man-roxygen/labelledTreeParam.R man-roxygen/leftChildParam.R man-roxygen/mergeEdgesParam.R man-roxygen/morphyObjParam.R man-roxygen/nCoresParam.R man-roxygen/nTaxaParam.R
man-roxygen/outgroupTipsParam
man-roxygen/outgroupTipsParam.R man-roxygen/parentOfParam.R man-roxygen/pointlessDots.R man-roxygen/preorderTreeParam.r man-roxygen/returnEdgeList.R man-roxygen/returnPhydat.R man-roxygen/rightChildParam.R man-roxygen/sessionParam.R man-roxygen/splitsParam.R man-roxygen/stopAtPeakParam.R man-roxygen/stopAtPlateauParam.R man-roxygen/stopAtScoreParam.R man-roxygen/swappersParam.R man-roxygen/treeChild.R man-roxygen/treeNEdge.R man-roxygen/treeNEdgeOptional.R man-roxygen/treeParam.r man-roxygen/treeParent.r man-roxygen/treeScorerDots.r man-roxygen/treeScorerParam.r man-roxygen/verbosityParam.r man-roxygen/warnParam.R man/AddTip.Rd man/AllAncestors.Rd man/AllSPR.Rd man/AncestorEdge.Rd man/ApeTime.Rd man/AsBinary.Rd man/C_node_depth.Rd man/CladeSizes.Rd man/Cladewise.Rd man/CollapseNode.Rd man/ConsensusWithout.Rd man/DFact.Rd man/DescendantEdges.Rd man/DoubleNNI.Rd man/DropSingleSplits.Rd man/EdgeAncestry.Rd man/EnforceOutgroup.Rd man/Evaluate.Rd man/ExtractTaxa.Rd man/Fitch.Rd man/FitchSteps.Rd man/ICPerStep.Rd man/ICSteps.Rd man/IWScore.Rd man/InfoAmounts.Rd man/LDFact.Rd man/LDFactorial.Rd man/ListToMatrix.Rd man/Lobo.data.Rd man/Lobo.phy.Rd man/LogisticPoints.Rd man/MatrixToList.Rd man/MatrixToPhyDat.Rd man/MinimumSteps.Rd man/MorphyBootstrap.Rd man/MorphyErrorCheck.Rd man/MorphyTreeLength.Rd man/MorphyWeights.Rd man/N1Spr.Rd man/NJTree.Rd man/NNI.Rd man/NRooted.Rd man/NamedConstant.Rd man/NewickTree.Rd man/NeworderPhylo.Rd man/NeworderPruningwise.Rd man/NonDuplicateRoot.Rd man/OrderEdgesNumberNodes.Rd man/PhyDat2Morphy.Rd man/PhyToString.Rd man/PrepareDataProfile.Rd man/ProfileScore.Rd man/RandomMorphyTree.Rd man/RandomTree.Rd man/RandomTreeScore.Rd man/Ratchet.Rd man/ReadCharacters.Rd man/ReadTntTree.Rd man/RearrangeEdges.Rd man/Renumber.Rd man/RenumberTips.Rd man/RenumberTree.Rd man/RightmostCharacter.Rd man/RootTree.Rd man/SPR.Rd man/SampleOne.Rd man/SetMorphyWeights.Rd man/SingleCharMorphy.Rd man/SingleTaxonTree.Rd man/SortTree.Rd man/SplitFrequency.Rd man/SplitsRepeated.Rd man/StringToPhyDat.Rd man/Suboptimality.Rd man/Subtree.Rd man/SuccessiveApproximations.Rd man/SuccessiveWeights.Rd man/SupportColour.Rd man/TBR.Rd man/TBRWarning.Rd man/TipsAreNames.Rd man/Tree2Splits.Rd man/TreeSearch.Rd man/UniqueExceptHits.Rd man/UniqueSplits.Rd man/UnloadMorphy.Rd man/UnloadTreeSearch.Rd man/WithOneExtraStep.Rd man/brewer.Rd man/congreveLamsdellMatrices.Rd man/inapplicable.citations.Rd man/inapplicable.datasets.Rd man/inapplicable.phyData.Rd man/mpl_apply_tipdata.Rd man/mpl_attach_rawdata.Rd man/mpl_attach_symbols.Rd man/mpl_delete_Morphy.Rd man/mpl_delete_rawdata.Rd man/mpl_first_down_recon.Rd man/mpl_first_up_recon.Rd man/mpl_get_charac_weight.Rd man/mpl_get_num_charac.Rd man/mpl_get_num_internal_nodes.Rd man/mpl_get_numtaxa.Rd man/mpl_get_symbols.Rd man/mpl_init_Morphy.Rd man/mpl_new_Morphy.Rd man/mpl_second_down_recon.Rd man/mpl_second_up_recon.Rd man/mpl_set_charac_weight.Rd man/mpl_set_num_internal_nodes.Rd man/mpl_set_parsim_t.Rd man/mpl_translate_error.Rd man/mpl_update_lower_root.Rd man/mpl_update_tip.Rd man/referenceTree.Rd man/summary.morphyPtr.Rd
src/RMorphy.c
src/RMorphy.h
src/RMorphyUtils.c
src/RMorphyUtils.h
src/RcppExports.cpp
src/TreeSearch-init.c
src/ape_reorder.h
src/build_postorder.h
src/fitch.c
src/fitch.h
src/from_ape.c
src/morphy.c
src/morphy.h
src/morphydefs.h
src/mpl.c
src/mpl.h
src/mplerror.h
src/phangorn_bip.cpp
src/renumber_tree.h
src/statedata.c
src/statedata.h
src/wagner.c
src/wagner.h
tests/testthat.R tests/testthat/test-Partitions.R tests/testthat/test-Support.R tests/testthat/test-ape-interface.R
tests/testthat/test-ape-tree.nex
tests/testthat/test-data-manipulation.R tests/testthat/test-mpl-counts.R tests/testthat/test-mpl-search.R
tests/testthat/test-parse-nexus.nexus
tests/testthat/test-parsers.R tests/testthat/test-pp-ICS.R tests/testthat/test-pp-fitch.R tests/testthat/test-pp-random-tree.R tests/testthat/test-pp-search.R
tests/testthat/test-tnt-matrix.tnt
tests/testthat/test-tnt-tree.tre
tests/testthat/test-tree-functions.R tests/testthat/test-tree-rearrange.R tests/testthat/test-tree-rearranged-numbering.R vignettes/getting-started.Rmd vignettes/inapplicable.Rmd vignettes/load-data.Rmd vignettes/profile-scores.Rmd vignettes/profile.Rmd
ms609/TreeSearch documentation built on Dec. 8, 2018, 4:23 p.m.