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.

Install the latest version of this package by entering the following in R:
install.packages("paleotree")
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

Functions

addTermBranchLength Man page
ancPropStateMat Man page
bin_cal3TimePaleoPhy Man page
bindPaleoTip Man page
binTimeData Man page
bin_timePaleoPhy Man page
branchClasses Man page
cal3 Man page
cal3TimePaleoPhy Man page
candleTaxa Man page
charMatDicrano Man page
cladogeneticTraitCont Man page
cladogramDicrano Man page
cleanNewPhylo Man page
cleanTree Man page
collapseNodes Man page
communityEcology Man page
compareNodeAges Man page
compareTermBranches Man page
compareTimescaling Man page
constrainParPaleo Man page
createMrBayesConstraints Man page
dateNodes Man page
deadTree Man page
degradeTree Man page
depthRainbow Man page
divCurveFossilRecordSim Man page
DiversityCurves Man page
dropExtant Man page
dropExtinct Man page
dropPaleoTip Man page
dropZLB Man page
durationFreq Man page
equation2function Man page
expandTaxonTree Man page
fixRootTime Man page
footeValues Man page
foramAL Man page
foramALb Man page
foramAM Man page
foramAMb Man page
fossilRecord2fossilRanges Man page
fossilRecord2fossilTaxa Man page
fourDate2timeList Man page
fourDateFunctions Man page
freqRat Man page
graptCharMatrix Man page
graptDisparity Man page
graptDistMat Man page
graptOccPBDB Man page
graptPBDB Man page
graptRanges Man page
graptTaxaPBDB Man page
horizonSampRate Man page
HurlbertPIE Man page
inverseSurv Man page
invSurv Man page
kanto Man page
macroperforateForam Man page
make_durationFreqCont Man page
make_durationFreqDisc Man page
make_inverseSurv Man page
makePBDBtaxonTree Man page
minBranchLength Man page
minCharChange Man page
modelMethods Man page
modifyTerminalBranches Man page
multiDiv Man page
nearestNeighborDist Man page
occData2timeList Man page
optimPaleo Man page
pairwiseSpearmanRho Man page
paleotree Man page
paleotree-package Man page
parbounds Man page
parbounds<- Man page
parbounds<-.constrained Man page
parbounds.constrained Man page
parbounds<-.paleotreeFunc Man page
parbounds.paleotreeFunc Man page
parentChild2taxonTree Man page
parInit Man page
parInit.constrained Man page
parInit.paleotreeFunc Man page
parLower Man page
parLower<- Man page
parLower<-.constrained Man page
parLower.constrained Man page
parLower<-.paleotreeFunc Man page
parLower.paleotreeFunc Man page
parnames Man page
parnames<- Man page
parnames<-.constrained Man page
parnames.constrained Man page
parnames<-.paleotreeFunc Man page
parnames.paleotreeFunc Man page
parUpper Man page
parUpper<- Man page
parUpper<-.constrained Man page
parUpper.constrained Man page
parUpper<-.paleotreeFunc Man page
parUpper.paleotreeFunc Man page
perCapitaRates Man page
perfectParsCharTree Man page
phyloDiv Man page
plotMultiDiv Man page
plotOccData Man page
plotTraitgram Man page
pqr2Ps Man page
pqsRate2sProb Man page
probAnc Man page
qsProb2Comp Man page
qsRate2Comp Man page
resolveTreeChar Man page
retioChar Man page
retiolitinae Man page
retioRanges Man page
retioTree Man page
reverseList Man page
rootSplit Man page
sampleRanges Man page
SamplingConv Man page
seqTimeList Man page
simCandleTaxa Man page
simFossilRecord Man page
simFossilRecordMethods Man page
simTermTaxa Man page
simTermTaxaAdvanced Man page
SongZhangDicrano Man page
sProb2sRate Man page
sRate2sProb Man page
taxa2cladogram Man page
taxa2phylo Man page
taxicDivCont Man page
taxicDivDisc Man page
taxonSortPBDBocc Man page
taxonTable2taxonTree Man page
termTaxa Man page
testEdgeMat Man page
timeLadderTree Man page
timeList2fourDate Man page
timePaleoPhy Man page
timeSliceFossilRecord Man page
timeSliceTree Man page
trueCandle Man page
trueTermTaxaTree Man page
unitLengthTree Man page

Files

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

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Please suggest features or report bugs with the GitHub issue tracker.

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