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paleotree  

Paleontological and Phylogenetic Analyses of Evolution
View on CRAN: Click here


Download and install paleotree package within the R console
Install from CRAN:
install.packages("paleotree")

Install from Github:
library("remotes")
install_github("cran/paleotree")

Install by package version:
library("remotes")
install_version("paleotree", "3.4.7")



Attach the package and use:
library("paleotree")
Maintained by
David W. Bapst
[Scholar Profile | Author Map]
First Published: 2012-01-27
Latest Update: 2022-08-22
Description:
Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.
How to cite:
David W. Bapst (2012). paleotree: Paleontological and Phylogenetic Analyses of Evolution. R package version 3.4.7, https://cran.r-project.org/web/packages/paleotree. Accessed 07 Apr. 2025.
Previous versions and publish date:
1.0 (2012-01-27 12:09), 1.1 (2012-02-13 07:43), 1.2 (2012-02-23 18:24), 1.3 (2012-04-19 07:39), 1.4 (2012-06-18 09:00), 1.5 (2012-10-06 16:11), 1.6 (2012-12-31 08:28), 1.7 (2012-12-31 19:57), 1.8.1 (2013-04-04 09:08), 1.8.2 (2013-09-04 23:17), 1.8 (2013-02-23 08:10), 1.9 (2014-01-03 07:45), 2.0 (2014-02-04 10:35), 2.1 (2014-08-16 09:55), 2.2 (2014-09-18 09:56), 2.3 (2015-01-16 18:12), 2.4 (2015-05-02 09:32), 2.5 (2015-09-21 11:19), 2.6 (2015-12-03 00:21), 2.7 (2016-04-13 21:35), 3.0.0 (2017-10-21 15:08), 3.1.0 (2018-07-03 06:10), 3.1.3 (2018-10-02 16:40), 3.3.0 (2019-06-05 00:20), 3.3.25 (2019-12-12 13:50), 3.4.4 (2022-04-25 12:10), 3.4.5 (2022-08-22 08:30)
Other packages that cited paleotree R package
View paleotree citation profile
Other R packages that paleotree depends, imports, suggests or enhances
Complete documentation for paleotree
Functions, R codes and Examples using the paleotree R package
Some associated functions: DiversityCurves . RaiaCopesRule . SamplingConv . SongZhangDicrano . binTimeData . branchClasses . cal3TimePaleoPhy . cladogeneticTraitCont . communityEcology . compareTimescaling . constrainParPaleo . createMrBayesConstraints . createMrBayesTipCalibrations . createMrBayesTipDatingNexus . dateNodes . dateTaxonTreePBDB . degradeTree . depthRainbow . divCurveFossilRecordSim . durationFreq . equation2function . exhaustionFunctions . expandTaxonTree . fixRootTime . footeValues . freqRat . getDataPBDB . graptDisparity . graptPBDB . horizonSampRate . inverseSurv . kanto . macroperforateForam . makePBDBtaxonTree . minBranchLength . minCharChange . modelMethods . modifyTerminalBranches . multiDiv . nearestNeighborDist . nodeDates2branchLengths . obtainDatedPosteriorTreesMrB . occData2timeList . optimPaleo . paleotree-package . parentChild2taxonTree . perCapitaRates . perfectParsCharTree . plotOccData . plotPhyloPicTree . plotTraitgram . pqr2Ps . probAnc . resolveTreeChar . retiolitinae . reverseList . rootSplit . sampleRanges . seqTimeList . setRootAge . simFossilRecord . simFossilRecordMethods . taxa2cladogram . taxa2phylo . taxonSortPBDBocc . taxonTable2taxonTree . termTaxa . testEdgeMat . timeLadderTree . timeList2fourDate . timePaleoPhy . timeSliceTree . tipDatingCompatabilitySummaryMrB . treeContradiction . twoWayEcologyCluster . unitLengthTree . 
Some associated R codes: DiversityCurves.R . RaiaCopesRule.R . SamplingConv.R . SongZhangDicrano.R . binTimeData.R . branchClasses.R . cal3TimePaleoPhy.R . cladogeneticTraitCont.R . communityEcology.R . compareTimescaling.R . constrainParPaleo.R . createMrBayesConstraints.R . createMrBayesTipCalibrations.R . createMrBayesTipDatingNexus.R . dateNodes.R . dateTaxonTreePBDB.R . degradeTree.R . depthRainbow.R . divCurveFossilRecordSim.R . durationFreq.R . equation2function.R . exhaustationFunctions.R . expandTaxonTree.R . fixRootTime.R . footeValues.R . fourDateFunctions.R . freqRat.R . getDataPBDB.R . getFixedAgesFromNexus.R . graptDisparity.R . graptPBDB.R . hidden.gettingPhyloPicFunctions.R . hidden.makePBDBtaxonTree.Functions.R . hidden.modelExpressionModification.R . hidden.plotTaxonStratDurations.R . hidden.plottingPhyloPicFunctions.R . horizonSampRate.R . inverseSurv.R . isTimeListSequential.R . kanto.R . macroperforateForam.R . makePBDBtaxonTree.R . minBranchLength.R . minCharChange.R . modelMethods.R . modifyTerminalBranches.R . multiDiv.R . nearestNeighborDist.R . nodeDates2branchLengths.R . obtainDatedPosteriorTreesMrB.R . occData2timeList.R . optimPaleo.R . paleotree-package.R . parentChild2TaxonTree.R . parseNexusFile.R . perCapitaRates.R . perfectParsCharTree.R . plotOccData.R . plotPhyloPicTree.R . plotTraitgram.R . pqr2Ps.R . probAnc.R . resolveTreeChar.R . retiolitinae.R . reverseList.R . rootSplit.R . sampleRanges.R . seqTimeList.R . setRootAge.R . simFossilRecord.R . simFossilRecordInternal.R . simFossilRecordMethods.R . taxa2cladogram.R . taxa2phylo.R . taxonSortPBDBocc.R . taxonTable2TaxonTree.R . termTaxa.R . testEdgeMat.R . timeLadderTree.R . timePaleoPhy.R . timeSliceTree.R . tipDatingCompatabilitySummaryMrB.R . treeContradiction.R . twoWayEcologyCluster.R . unitLengthTree.R . writeSimpleSumtNexus.R .  Full paleotree package functions and examples
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