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 a posteriori time-scale cladograms of fossil taxa into dated phylogenies. 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.

AuthorDavid W. Bapst
Date of publication2016-04-13 21:35:16
MaintainerDavid W. Bapst <dwbapst@gmail.com>
LicenseCC0
Version2.7
https://github.com/dwbapst/paleotree , http://webpages.sdsmt.edu/~dbapst/

View on CRAN

Man pages

binTimeData: Bin Simulated Temporal Ranges in Discrete Intervals

branchClasses: Partitions the branch lengths of a tree into several classes...

cal3TimePaleoPhy: Three Rate Calibrated 'a posteriori' Time-Scaling of...

cladogeneticTraitCont: Simulate Cladogenetic Trait Evolution

communityEcology: Miscellaneous Functions for Community Ecology

compareTimescaling: Comparing the Time-Scaling of Trees

constrainParPaleo: Constrain Parameters for a Model Function from paleotree

createMrBayesConstraints: Transform a Topology into a Set of Constraint Commands for...

dateNodes: Absolute Dates for Nodes of a Time-Scaled Phylogeny

degradeTree: Randomly Collapse a Portion of Nodes on a Phylogeny

depthRainbow: Paint Tree Branch Depth by Color

divCurveFossilRecordSim: Diversity-Curve Plotting for Simulations of Diversification...

DiversityCurves: Diversity Curves

durationFreq: Models of Sampling and Extinction for Taxonomic Duration...

equation2function: Turn a Character String of the Right-Hand Side of an Equation...

expandTaxonTree: Extrapolating Lower-Level Taxon Phylogenies from Higher-Level...

footeValues: Calculates Values for Foote's Inverse Survivorship Analyses

freqRat: Frequency Ratio Method for Estimating Sampling Probability

graptDisparity: Morphlogical Character and Range Data for late Ordovician and...

graptPBDB: Example Occurrence and Taxonomic Datasets of the...

horizonSampRate: Estimate Sampling Rate from Sampling Horizon Data (Solow and...

inverseSurv: Inverse Survivorship Models in the Fossil Record

kanto: Example Species Abundances Tables

macroperforateForam: Ancestor-Descendant Relationships for Macroperforate...

makePBDBtaxonTree: Creating a Taxon-Tree from Taxonomic Data Downloaded from the...

minBranchLength: Scales Edge Lengths of a Phylogeny to a Minimum Branch Length

minCharChange: Estimating the Minimum Number of Character Transitions Using...

modelMethods: Model Function Methods: Parameter Names, Bounds and Initial...

modifyTerminalBranches: Modify, Drop or Bind Terminal Branches of Various Types...

multiDiv: Calculating Diversity Curves Across Multiple Datasets

nearestNeighborDist: Nearest Neighbor Distances for Morphological Disparity...

occData2timeList: Converting Occurrences Data to a timeList Data Object

optimPaleo: Simplified Optimizer for paleotree Likelihood Functions

paleotree-package: paleotree: Paleontological and Phylogenetic Analyses of...

parentChild2taxonTree: Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table...

perCapitaRates: perCapitaRates

perfectParsCharTree: Simulate a Set of Parsimony-Informative Characters for a...

plotOccData: Plotting Occurrence Data Across Taxa

plotTraitgram: Plot a Traitgram for Continuous Traits

pqr2Ps: Joint Probability of A Clade Surviving Infinitely or Being...

probAnc: Probability of being a sampled ancestor of another sampled...

resolveTreeChar: Resolve Polytomies Using Parsimony-Based Reconstruction of a...

retiolitinae: Cladogram and Range Data for the Retiolitinae

reverseList: Reverse List Structure

rootSplit: Split Tip Taxa by Root Divergence

sampleRanges: Sampling Taxon Ranges

SamplingConv: Converting Sampling Estimates

seqTimeList: Construct a Stochastic Sequenced Time-List from an...

simFossilRecord: Full-Scale Simulations of the Fossil Record with Birth, Death...

simFossilRecordMethods: Methods for Editing or Converting Output from simFossilRecord

SongZhangDicrano: Cladistic Data for Dicranograptid Graptolites from Song and...

taxa2cladogram: Convert Simulated Taxon Data into a Cladogram

taxa2phylo: Convert Simulated Taxon Data into a Phylogeny

taxonSortPBDBocc: Sorting Unique Taxa of a Given Rank from Paleobiology...

taxonTable2taxonTree: Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a...

termTaxa: Simulating Extinct Clades of Monophyletic Taxa

testEdgeMat: Test the Edge Matrix of a 'phylo' Phylogeny Object for...

timeLadderTree: Resolve Polytomies by Order of First Appearance

timeList2fourDate: Converting Datasets of Taxon Ranges in Intervals Between...

timePaleoPhy: Typical 'a posteriori' Time-Scaling Approaches For...

timeSliceTree: Time-Slicing a Phylogeny

unitLengthTree: Scale Tree to Unit-Length

Files in this package

paleotree
paleotree/inst
paleotree/inst/CITATION
paleotree/tests
paleotree/tests/minBranchLength_check_10-09-15.R
paleotree/NAMESPACE
paleotree/CHANGELOG
paleotree/data
paleotree/data/macroperforateForam.rdata
paleotree/data/SongZhangDicrano.rdata
paleotree/data/graptDisparity.rdata
paleotree/data/retiolitinae.rdata
paleotree/data/graptPBDB.rdata
paleotree/data/kanto.rdata
paleotree/R
paleotree/R/expandTaxonTree.R paleotree/R/freqRat.R paleotree/R/retiolitinae.R paleotree/R/pqr2Ps.R paleotree/R/hiddenFunctions.R paleotree/R/simFossilRecordInternal.R paleotree/R/modelMethods.R paleotree/R/createMrBayesConstraints.R paleotree/R/DiversityCurves.R paleotree/R/SongZhangDicrano.R paleotree/R/makePBDBtaxonTree.R paleotree/R/branchClasses.R paleotree/R/kanto.R paleotree/R/seqTimeList.R paleotree/R/fourDateFunctions.R paleotree/R/timeSliceTree.R paleotree/R/taxa2cladogram.R paleotree/R/multiDiv.R paleotree/R/occData2timeList.R paleotree/R/graptDisparity.R paleotree/R/dateNodes.R paleotree/R/perCapitaRates.R paleotree/R/testEdgeMat.R paleotree/R/footeValues.R paleotree/R/simFossilRecordMethods.R paleotree/R/plotOccData.R paleotree/R/unitLengthTree.R paleotree/R/degradeTree.R paleotree/R/cal3TimePaleoPhy.R paleotree/R/inverseSurv.R paleotree/R/modifyTerminalBranches.R paleotree/R/simFossilRecord.R paleotree/R/macroperforateForam.R paleotree/R/equation2function.R paleotree/R/divCurveFossilRecordSim.R paleotree/R/taxa2phylo.R paleotree/R/constrainParPaleo.R paleotree/R/rootSplit.R paleotree/R/probAnc.R paleotree/R/timePaleoPhy.R paleotree/R/minBranchLength.R paleotree/R/SamplingConv.R paleotree/R/taxonTable2taxonTree.R paleotree/R/reverseList.R paleotree/R/resolveTreeChar.R paleotree/R/termTaxa.R paleotree/R/depthRainbow.R paleotree/R/horizonSampRate.R paleotree/R/compareTimescaling.R paleotree/R/plotTraitgram.R paleotree/R/minCharChange.R paleotree/R/parentChild2taxonTree.R paleotree/R/timeLadderTree.R paleotree/R/nearestNeighborDist.R paleotree/R/optimPaleo.R paleotree/R/communityEcology.R paleotree/R/cladogeneticTraitCont.R paleotree/R/taxonSortPBDBocc.R paleotree/R/paleotree-package.R paleotree/R/perfectParsCharTree.R paleotree/R/graptPBDB.R paleotree/R/sampleRanges.R paleotree/R/binTimeData.R paleotree/R/durationFreq.R
paleotree/MD5
paleotree/README
paleotree/DESCRIPTION
paleotree/man
paleotree/man/DiversityCurves.Rd paleotree/man/multiDiv.Rd paleotree/man/footeValues.Rd paleotree/man/dateNodes.Rd paleotree/man/binTimeData.Rd paleotree/man/timeLadderTree.Rd paleotree/man/cladogeneticTraitCont.Rd paleotree/man/equation2function.Rd paleotree/man/depthRainbow.Rd paleotree/man/perfectParsCharTree.Rd paleotree/man/taxonTable2taxonTree.Rd paleotree/man/minBranchLength.Rd paleotree/man/graptDisparity.Rd paleotree/man/durationFreq.Rd paleotree/man/communityEcology.Rd paleotree/man/nearestNeighborDist.Rd paleotree/man/degradeTree.Rd paleotree/man/probAnc.Rd paleotree/man/modelMethods.Rd paleotree/man/kanto.Rd paleotree/man/simFossilRecord.Rd paleotree/man/retiolitinae.Rd paleotree/man/seqTimeList.Rd paleotree/man/parentChild2taxonTree.Rd paleotree/man/horizonSampRate.Rd paleotree/man/plotOccData.Rd paleotree/man/macroperforateForam.Rd paleotree/man/SongZhangDicrano.Rd paleotree/man/compareTimescaling.Rd paleotree/man/timePaleoPhy.Rd paleotree/man/taxa2phylo.Rd paleotree/man/cal3TimePaleoPhy.Rd paleotree/man/optimPaleo.Rd paleotree/man/testEdgeMat.Rd paleotree/man/makePBDBtaxonTree.Rd paleotree/man/sampleRanges.Rd paleotree/man/createMrBayesConstraints.Rd paleotree/man/constrainParPaleo.Rd paleotree/man/expandTaxonTree.Rd paleotree/man/unitLengthTree.Rd paleotree/man/simFossilRecordMethods.Rd paleotree/man/paleotree-package.Rd paleotree/man/freqRat.Rd paleotree/man/divCurveFossilRecordSim.Rd paleotree/man/inverseSurv.Rd paleotree/man/occData2timeList.Rd paleotree/man/modifyTerminalBranches.Rd paleotree/man/reverseList.Rd paleotree/man/rootSplit.Rd paleotree/man/minCharChange.Rd paleotree/man/taxonSortPBDBocc.Rd paleotree/man/resolveTreeChar.Rd paleotree/man/taxa2cladogram.Rd paleotree/man/timeList2fourDate.Rd paleotree/man/branchClasses.Rd paleotree/man/perCapitaRates.Rd paleotree/man/timeSliceTree.Rd paleotree/man/termTaxa.Rd paleotree/man/pqr2Ps.Rd paleotree/man/graptPBDB.Rd paleotree/man/SamplingConv.Rd paleotree/man/plotTraitgram.Rd

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