Files in paleotree

Paleontological and Phylogenetic Analyses of Evolution

README.md R/twoWayEcologyCluster.R R/communityEcology.R R/durationFreq.R R/probAnc.R R/cladogeneticTraitCont.R R/SamplingConv.R R/graptPBDB.R R/testEdgeMat.R R/termTaxa.R R/parseNexusFile.R R/createMrBayesConstraints.R R/equation2function.R R/hidden.modelExpressionModification.R R/reverseList.R R/tipDatingCompatabilitySummaryMrB.R R/plotTraitgram.R R/DiversityCurves.R R/compareTimescaling.R R/dateNodes.R R/makePBDBtaxonTree.R R/minCharChange.R R/fixRootTime.R R/timeLadderTree.R R/expandTaxonTree.R R/timePaleoPhy.R R/taxonSortPBDBocc.R R/fourDateFunctions.R R/plotOccData.R R/writeSimpleSumtNexus.R R/parentChild2TaxonTree.R R/obtainDatedPosteriorTreesMrB.R R/graptDisparity.R R/sampleRanges.R R/hidden.plotTaxonStratDurations.R R/branchClasses.R R/optimPaleo.R R/macroperforateForam.R R/getFixedAgesFromNexus.R R/hidden.plottingPhyloPicFunctions.R R/timeSliceTree.R R/simFossilRecordMethods.R R/seqTimeList.R R/constrainParPaleo.R R/paleotree-package.R R/retiolitinae.R R/nearestNeighborDist.R R/modifyTerminalBranches.R R/SongZhangDicrano.R R/RaiaCopesRule.R R/kanto.R R/freqRat.R R/isTimeListSequential.R R/rootSplit.R R/createMrBayesTipCalibrations.R R/hidden.makePBDBtaxonTree.Functions.R R/taxa2cladogram.R R/cal3TimePaleoPhy.R R/perfectParsCharTree.R R/simFossilRecord.R R/exhaustationFunctions.R R/resolveTreeChar.R R/perCapitaRates.R R/inverseSurv.R R/divCurveFossilRecordSim.R R/simFossilRecordInternal.R R/createMrBayesTipDatingNexus.R R/treeContradiction.R R/plotPhyloPicTree.R R/occData2timeList.R R/dateTaxonTreePBDB.R R/hidden.gettingPhyloPicFunctions.R R/degradeTree.R R/horizonSampRate.R R/getDataPBDB.R R/unitLengthTree.R R/depthRainbow.R R/modelMethods.R R/taxa2phylo.R R/taxonTable2TaxonTree.R R/multiDiv.R R/setRootAge.R R/pqr2Ps.R R/footeValues.R R/binTimeData.R R/nodeDates2branchLengths.R R/minBranchLength.R tests/testthat.R tests/spelling.R tests/testthat/test_timeSlice_dropExtinct_shifts_root_age.R tests/testthat/test_simFossilRecord_simple.R tests/testthat/test_obtainDatedPosteriorTreesMrB.R tests/testthat/test_cal3_dateTreatment_Armin.R tests/testthat/test_Contradiction_05-25-17.R tests/testthat/test_cladogeneticTraitCont.R tests/testthat/test_simFossilRecord_returnAllRuns_output.R tests/testthat/test_simFossilRecord_countFinalTaxa_07-15-19.R tests/testthat/test_simFossilRecord_return_extant_taxa.R tests/testthat/test_minBranchLength_check_10-09-15.R tests/testthat/test_simFossilRecord_return_extinct_taxa.R tests/testthat/test_simFossilRecord_rejection.R tests/testthat/test_simFossilRecord_negative_dates_07-06-19.R tests/testthat/test_inverseSurv.R tests/testthat/test_timeSlice_tip_labels_differ.R man/perCapitaRates.Rd man/sampleRanges.Rd man/parentChild2taxonTree.Rd man/rootSplit.Rd man/testEdgeMat.Rd man/minBranchLength.Rd man/communityEcology.Rd man/RaiaCopesRule.Rd man/SamplingConv.Rd man/inverseSurv.Rd man/fixRootTime.Rd man/minCharChange.Rd man/nodeDates2branchLengths.Rd man/cal3TimePaleoPhy.Rd man/timeList2fourDate.Rd man/taxonSortPBDBocc.Rd man/graptPBDB.Rd man/createMrBayesConstraints.Rd man/kanto.Rd man/timeSliceTree.Rd man/perfectParsCharTree.Rd man/plotTraitgram.Rd man/nearestNeighborDist.Rd man/termTaxa.Rd man/expandTaxonTree.Rd man/durationFreq.Rd man/dateTaxonTreePBDB.Rd man/makePBDBtaxonTree.Rd man/dateNodes.Rd man/taxa2cladogram.Rd man/getDataPBDB.Rd man/paleotree-package.Rd man/modelMethods.Rd man/cladogeneticTraitCont.Rd man/twoWayEcologyCluster.Rd man/unitLengthTree.Rd man/taxa2phylo.Rd man/reverseList.Rd man/timeLadderTree.Rd man/createMrBayesTipDatingNexus.Rd man/setRootAge.Rd man/constrainParPaleo.Rd man/graptDisparity.Rd man/pqr2Ps.Rd man/simFossilRecordMethods.Rd man/horizonSampRate.Rd man/seqTimeList.Rd man/degradeTree.Rd man/treeContradiction.Rd man/resolveTreeChar.Rd man/modifyTerminalBranches.Rd man/plotOccData.Rd man/depthRainbow.Rd man/macroperforateForam.Rd man/equation2function.Rd man/DiversityCurves.Rd man/compareTimescaling.Rd man/obtainDatedPosteriorTreesMrB.Rd man/simFossilRecord.Rd man/createMrBayesTipCalibrations.Rd man/occData2timeList.Rd man/timePaleoPhy.Rd man/branchClasses.Rd man/tipDatingCompatabilitySummaryMrB.Rd man/taxonTable2taxonTree.Rd man/plotPhyloPicTree.Rd man/optimPaleo.Rd man/freqRat.Rd man/footeValues.Rd man/binTimeData.Rd man/divCurveFossilRecordSim.Rd man/multiDiv.Rd man/probAnc.Rd man/SongZhangDicrano.Rd man/retiolitinae.Rd man/exhaustionFunctions.Rd