Package: paleotree 3.4.7

David W. Bapst

paleotree: Paleontological and Phylogenetic Analyses of Evolution

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.

Authors:David W. Bapst, Peter J. Wagner

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paleotree.pdf |paleotree.html✨
paleotree/json (API)

# Install 'paleotree' in R:
install.packages('paleotree', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dwbapst/paleotree/issues

Datasets:
  • ammoniteTraitsRaia - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
  • ammoniteTreeRaia - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
  • ceratopsianTreeRaia - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
  • cervidTreeRaia - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
  • charMatDicrano - Cladistic Data for Dicranograptid Graptolites from Song and Zhang
  • cladogramDicranoX12 - Cladistic Data for Dicranograptid Graptolites from Song and Zhang
  • cladogramDicranoX13 - Cladistic Data for Dicranograptid Graptolites from Song and Zhang
  • foramAL - Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al.
  • foramALb - Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al.
  • foramAM - Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al.
  • foramAMb - Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al.
  • graptCharMatrix - Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
  • graptDistMat - Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
  • graptOccPBDB - Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
  • graptRanges - Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
  • graptTaxaPBDB - Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
  • graptTimeTree - Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
  • graptTree - Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology Database
  • kanto - Example Species Abundances Tables
  • retioChar - Cladogram and Range Data for the Retiolitinae
  • retioRanges - Cladogram and Range Data for the Retiolitinae
  • retioTree - Cladogram and Range Data for the Retiolitinae
  • shellSize - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
  • sutureComplexity - Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015

On CRAN:

109 exports 21 stars 4.11 score 57 dependencies 4 dependents 21 mentions 211 scripts 1.3k downloads

Last updated 2 months agofrom:72ad91ba4c. Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 07 2024
R-4.5-winNOTESep 07 2024
R-4.5-linuxNOTESep 07 2024
R-4.4-winNOTESep 07 2024
R-4.4-macNOTESep 07 2024
R-4.3-winNOTESep 07 2024
R-4.3-macNOTESep 07 2024

Exports:accioBestAcquisitionModelaccioExhaustionCurveaddTermBranchLengthancPropStateMatbin_cal3TimePaleoPhybin_timePaleoPhybindPaleoTipbinTimeDatabranchClassescal3TimePaleoPhycharExhaustPlotcladogeneticTraitContcleanNewPhylocollapseNodescompareNodeAgescompareTermBranchesconstrainParPaleocreateMrBayesConstraintscreateMrBayesTipCalibrationscreateMrBayesTipDatingNexusdateNodesdateTaxonTreePBDBdeadTreedegradeTreedepthRainbowdivCurveFossilRecordSimdropExtantdropExtinctdropPaleoTipdropZLBequation2functionexpandTaxonTreefixRootTimefooteValuesfossilRecord2fossilRangesfossilRecord2fossilTaxafossilTaxa2fossilRecordfourDate2timeListfreqRatgetCladeTaxaPBDBgetPBDBoccgetSpecificTaxaPBDBhorizonSampRateHurlbertPIEmake_durationFreqContmake_durationFreqDiscmake_inverseSurvmakePBDBtaxonTreeminBranchLengthminCharChangemultiDivnearestNeighborDistnodeDates2branchLengthsobtainDatedPosteriorTreesMrBoccData2timeListoptimPaleopairwiseSpearmanRhoparboundsparbounds<-parentChild2taxonTreeparInitparLowerparLower<-parnamesparnames<-parUpperparUpper<-perCapitaRatesperfectParsCharTreephyloDivplotMultiDivplotOccDataplotPhyloPicTreeplotTaxaTreePBDBplotTraitgrampqr2PspqsRate2sProbprobAncqsProb2CompqsRate2CompresolveTreeCharreverseListrootSplitsampleRangesseqTimeListsetRootAgesetRootAgessimFossilRecordsimTermTaxasimTermTaxaAdvancedsProb2sRatesRate2sProbtaxa2cladogramtaxa2phylotaxicDivConttaxicDivDisctaxonSortPBDBocctaxonTable2taxonTreetestEdgeMattimeLadderTreetimeList2fourDatetimePaleoPhytimeSliceFossilRecordtimeSliceTreetipDatingCompatabilitySummaryMrBtreeContradictiontrueTermTaxaTreetwoWayEcologyClusterunitLengthTree

Dependencies:apebitopscliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdigestdoParallelexpmfansifarverfastmatchforeachgenericsggplot2ggseqlogogluegtableigraphisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellnlmenumDerivoptimParallelphangornphytoolspillarpkgconfigpngquadprogR6RColorBrewerRcppRCurlrlangscalesscatterplot3dtibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
paleotree: Paleontological and Phylogenetic Analyses of Evolutionpaleotree-package paleotree
Bin Simulated Temporal Ranges in Discrete IntervalsbinTimeData
Partitions the branch lengths of a tree into several classes based on their placement.branchClasses
Three Rate Calibrated _a posteriori_ Dating of Paleontological Phylogeniesbin_cal3TimePaleoPhy cal3 cal3TimePaleoPhy
Simulate Cladogenetic Trait EvolutioncladogeneticTraitCont
Miscellaneous Functions for Community EcologycommunityEcology HurlbertPIE pairwiseSpearmanRho PIE ProbabilityInterspecificEncounter
Comparing the Time-Scaling of TreescompareNodeAges compareTermBranches compareTimescaling
Constrain Parameters for a Model Function from paleotreeconstrainParPaleo
Transform a Topology into a Set of Constraint Commands for MrBayescreateMrBayesConstraints
Construct A Block of Tip Age Calibrations for Use with Tip-Dating Analyses in MrBayescreateMrBayesTipCalibrations
Construct a Fully Formatted NEXUS Script for Performing Tip-Dating Analyses With MrBayescreateMrBayesTipDatingNexus tipdating
Absolute Dates for Nodes of a Time-Scaled PhylogenydateNodes
Date a Taxon-Topology from the Paleobiology Database Using Appearance Data from the APIdateTaxonTreePBDB
Randomly Collapse a Portion of Nodes on a PhylogenycollapseNodes degradeTree
Paint Tree Branch Depth by ColordepthRainbow
Diversity-Curve Plotting for Simulations of Diversification and Sampling In the Fossil RecorddivCurveFossilRecordSim
Diversity CurvesDiversityCurves phyloDiv taxicDivCont taxicDivDisc
Models of Sampling and Extinction for Taxonomic Duration DatasetsdurationFreq make_durationFreqCont make_durationFreqDisc
Turn a Character String of the Right-Hand Side of an Equation into an R Functionequation2function
Analyses of the exhaustion of Character States Over Evolutionary HistoryaccioBestAcquisitionModel accioExhaustionCurve charExhaustPlot exhaustionFunctions
Extrapolating Lower-Level Taxon Phylogenies from Higher-Level Taxon TreesexpandTaxonTree
Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)fixRootTime
Calculates Values for Foote's Inverse Survivorship AnalysesfooteValues
Frequency Ratio Method for Estimating Sampling ProbabilityfreqRat
Obtaining Data for Taxa or Occurrences From Paleobiology Database APIgetCladeTaxaPBDB getDataPBDB getPBDBocc getSpecificTaxaPBDB
Morphlogical Character and Range Data for late Ordovician and Early Silurian GraptoloideagraptCharMatrix graptDisparity graptDistMat graptRanges
Example Occurrence and Taxonomic Datasets of the Graptolithina from the Paleobiology DatabasegraptOccPBDB graptPBDB graptTaxaPBDB graptTimeTree graptTree
Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 1997)horizonSampRate
Inverse Survivorship Models in the Fossil RecordinverseSurv invSurv make_inverseSurv
Example Species Abundances Tableskanto
Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)foramAL foramALb foramAM foramAMb macroperforateForam
Creating a Taxon-Tree from Taxonomic Data Downloaded from the Paleobiology DatabasemakePBDBtaxonTree plotTaxaTreePBDB
Scales Edge Lengths of a Phylogeny to a Minimum Branch LengthminBranchLen minBranchLength minimumBranchLen minimumBranchLength
Estimating the Minimum Number of Character Transitions Using Maximum ParsimonyancPropStateMat minCharChange
Model Function Methods: Parameter Names, Bounds and Initial ValuesmodelMethods parbounds parbounds.constrained parbounds.paleotreeFunc parbounds<- parbounds<-.constrained parbounds<-.paleotreeFunc parInit parInit.constrained parInit.paleotreeFunc parLower parLower.constrained parLower.paleotreeFunc parLower<- parLower<-.constrained parLower<-.paleotreeFunc parnames parnames.constrained parnames.paleotreeFunc parnames<- parnames<-.constrained parnames<-.paleotreeFunc parUpper parUpper.constrained parUpper.paleotreeFunc parUpper<- parUpper<-.constrained parUpper<-.paleotreeFunc
Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)addTermBranchLength bindPaleoTip dropExtant dropExtinct dropPaleoTip dropZLB modifyTerminalBranches
Calculating Diversity Curves Across Multiple DatasetsmultiDiv plotMultiDiv
Nearest Neighbor Distances for Morphological Disparity StudiesnearestNeighborDist
Obtaining Edge Lengths for Undated Phylogenies Using Known Branching Node and Tip AgesnodeDates2branchLengths
Get the Sample of Posterior Trees from a Dated Phylogenetic Analysis with MrBayes (Or a Summary Tree, such as the MCCT)obtainDatedPosteriorTreesMrB
Converting Occurrences Data to a 'timeList' Data ObjectoccData2timeList
Simplified Optimizer for 'paleotree' Likelihood FunctionsoptimPaleo
Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table of Parent-Child Taxon RelationshipsparentChild2taxonTree
Instantaneous _per-Capita_ Rates of Origination and Extinction from the Fossil RecordperCapitaRates
Simulate a Set of Parsimony-Informative Characters for a PhylogenyperfectParsCharTree
Plotting Occurrence Data Across TaxaplotOccData
Plot a Phylogeny with Organismal Silhouettes from PhyloPic, Called Via the Paleobiology Database APIplotPhyloPicTree
Plot a Traitgram for Continuous TraitsplotTraitgram
Joint Probability of A Clade Surviving Infinitely or Being Sampled Oncepqr2Ps
Probability of being a sampled ancestor of another sampled taxonprobAnc
Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015ammoniteTraitsRaia ammoniteTreeRaia ceratopsianTreeRaia cervidTreeRaia RaiaCopesRule shellSize sutureComplexity
Resolve Polytomies Using Parsimony-Based Reconstruction of a Discrete CharacterresolveTreeChar
Cladogram and Range Data for the RetiolitinaeretioChar retiolitinae retioRanges retioTree
Reverse List StructurereverseList
Split Tip Taxa by Root DivergencerootSplit
Sampling Taxon RangessampleRanges
Converting Sampling EstimatespqsRate2sProb qsProb2Comp qsRate2Comp SamplingConv sProb2sRate sRate2sProb
Construct a Stochastic Sequenced Time-List from an Unsequenced Time-ListseqTimeList
Place a Non-Ultrametric Tree of Fossil Taxa on Absolute TimesetRootAge setRootAges
Full-Scale Simulations of the Fossil Record with Birth, Death and Sampling of MorphotaxasimFossilRecord
Methods for Editing or Converting Output from Simulated Fossil Record ObjectsfossilRecord2fossilRanges fossilRecord2fossilTaxa fossilTaxa2fossilRecord simFossilRecordMethods timeSliceFossilRecord
Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)charMatDicrano cladogramDicranoX12 cladogramDicranoX13 SongZhangDicrano
Convert Simulated Taxon Data into a Cladogramtaxa2cladogram
Convert Simulated Taxon Data into a Phylogenytaxa2phylo
Sorting Unique Taxa of a Given Rank from Paleobiology Database Occurrence DatataxonSortPBDBocc
Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Hierarchical Table of Taxonomy MembershipstaxonTable2taxonTree
Simulating Extinct Clades of Monophyletic TaxacandleTaxa deadTree simCandleTaxa simTermTaxa simTermTaxaAdvanced termTaxa trueCandle trueTermTaxaTree
Test the Edge Matrix of a ''phylo'' Phylogeny Object for InconsistenciescleanNewPhylo cleanTree testEdgeMat
Resolve Polytomies by Order of First AppearancetimeLadderTree
Converting Datasets of Taxon Ranges in Intervals Between 'timeList' format and 'fourDate' formatfourDate2timeList fourDateFunctions timeList2fourDate
Simplistic _a posteriori_ Dating Approaches For Paleontological Phylogeniesbin_timePaleoPhy timePaleoPhy
Time-Slicing a PhylogenytimeSliceTree
Get the Compatibility Summary Topology From a Tip-Dating Analysis with MrBayestipDatingCompatabilitySummaryMrB
Measure the Contradiction Difference Between Two Phylogenetic TopologiestreeContradiction
R-Mode vs Q-Mode Two-Way Cluster Analyses and Abundance Plot for Community Ecology DatatwoWayEcologyCluster
Scale Tree to Unit-LengthunitLengthTree