paleotree: Paleontological and Phylogenetic Analyses of Evolution

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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.

Author
David W. Bapst
Date of publication
2016-04-13 21:35:16
Maintainer
David W. Bapst <dwbapst@gmail.com>
License
CC0
Version
2.7
URLs

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