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paleotree
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", "3.4.5")
Attach the package and use:
library("paleotree")
Maintained by
David W. Bapst
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
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 3.4.5, https://cran.r-project.org/web/packages/paleotree
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)
Other packages that cited paleotree R package
View paleotree citation profile
Other R packages that paleotree depends,
imports, suggests or enhances
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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