# Paleontological and Phylogenetic Analyses of Evolution

## Documentation for package ‘paleotree’ version 3.4.5

- DESCRIPTION file.

## Help Pages

A B C D E F G H I K M N O P Q R S T U

paleotree-package | paleotree: Paleontological and Phylogenetic Analyses of Evolution

## -- A --

accioBestAcquisitionModel | Analyses of the exhaustion of Character States Over Evolutionary History
accioExhaustionCurve | Analyses of the exhaustion of Character States Over Evolutionary History
addTermBranchLength | Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
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
ancPropStateMat | Estimating the Minimum Number of Character Transitions Using Maximum Parsimony

## -- B --

bindPaleoTip | Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
binTimeData | Bin Simulated Temporal Ranges in Discrete Intervals
bin_cal3TimePaleoPhy | Three Rate Calibrated _a posteriori_ Dating of Paleontological Phylogenies
bin_timePaleoPhy | Simplistic _a posteriori_ Dating Approaches For Paleontological Phylogenies
branchClasses | Partitions the branch lengths of a tree into several classes based on their placement.

## -- C --

cal3 | Three Rate Calibrated _a posteriori_ Dating of Paleontological Phylogenies
cal3TimePaleoPhy | Three Rate Calibrated _a posteriori_ Dating of Paleontological Phylogenies
candleTaxa | Simulating Extinct Clades of Monophyletic Taxa
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
charExhaustPlot | Analyses of the exhaustion of Character States Over Evolutionary History
charMatDicrano | Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
cladogeneticTraitCont | Simulate Cladogenetic Trait Evolution
cladogramDicranoX12 | Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
cladogramDicranoX13 | Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
cleanNewPhylo | Test the Edge Matrix of a "phylo" Phylogeny Object for Inconsistencies
cleanTree | Test the Edge Matrix of a "phylo" Phylogeny Object for Inconsistencies
collapseNodes | Randomly Collapse a Portion of Nodes on a Phylogeny
communityEcology | Miscellaneous Functions for Community Ecology
compareNodeAges | Comparing the Time-Scaling of Trees
compareTermBranches | Comparing the Time-Scaling of Trees
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 MrBayes
createMrBayesTipCalibrations | Construct A Block of Tip Age Calibrations for Use with Tip-Dating Analyses in MrBayes
createMrBayesTipDatingNexus | Construct a Fully Formatted NEXUS Script for Performing Tip-Dating Analyses With MrBayes

## -- D --

dateNodes | Absolute Dates for Nodes of a Time-Scaled Phylogeny
dateTaxonTreePBDB | Date a Taxon-Topology from the Paleobiology Database Using Appearance Data from the API
deadTree | Simulating Extinct Clades of Monophyletic Taxa
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 and Sampling In the Fossil Record
DiversityCurves | Diversity Curves
dropExtant | Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
dropExtinct | Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
dropPaleoTip | Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
dropZLB | Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
durationFreq | Models of Sampling and Extinction for Taxonomic Duration Datasets

## -- E --

equation2function | Turn a Character String of the Right-Hand Side of an Equation into an R Function
exhaustionFunctions | Analyses of the exhaustion of Character States Over Evolutionary History
expandTaxonTree | Extrapolating Lower-Level Taxon Phylogenies from Higher-Level Taxon Trees

## -- F --

fixRootTime | Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
footeValues | Calculates Values for Foote's Inverse Survivorship Analyses
foramAL | Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
foramALb | Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
foramAM | Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
foramAMb | Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
fossilRecord2fossilRanges | Methods for Editing or Converting Output from Simulated Fossil Record Objects
fossilRecord2fossilTaxa | Methods for Editing or Converting Output from Simulated Fossil Record Objects
fossilTaxa2fossilRecord | Methods for Editing or Converting Output from Simulated Fossil Record Objects
fourDate2timeList | Converting Datasets of Taxon Ranges in Intervals Between 'timeList' format and 'fourDate' format
fourDateFunctions | Converting Datasets of Taxon Ranges in Intervals Between 'timeList' format and 'fourDate' format
freqRat | Frequency Ratio Method for Estimating Sampling Probability

## -- G --

getCladeTaxaPBDB | Obtaining Data for Taxa or Occurrences From Paleobiology Database API
getDataPBDB | Obtaining Data for Taxa or Occurrences From Paleobiology Database API
getPBDBocc | Obtaining Data for Taxa or Occurrences From Paleobiology Database API
getSpecificTaxaPBDB | Obtaining Data for Taxa or Occurrences From Paleobiology Database API
graptCharMatrix | Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea
graptDisparity | 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
graptPBDB | 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

## -- H --

horizonSampRate | Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 1997)
HurlbertPIE | Miscellaneous Functions for Community Ecology

## -- I --

inverseSurv | Inverse Survivorship Models in the Fossil Record
invSurv | Inverse Survivorship Models in the Fossil Record

## -- K --

kanto | Example Species Abundances Tables

## -- M --

macroperforateForam | Ancestor-Descendant Relationships for Macroperforate Foraminifera, from Aze et al. (2011)
makePBDBtaxonTree | Creating a Taxon-Tree from Taxonomic Data Downloaded from the Paleobiology Database
make_durationFreqCont | Models of Sampling and Extinction for Taxonomic Duration Datasets
make_durationFreqDisc | Models of Sampling and Extinction for Taxonomic Duration Datasets
make_inverseSurv | Inverse Survivorship Models in the Fossil Record
minBranchLen | Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
minBranchLength | Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
minCharChange | Estimating the Minimum Number of Character Transitions Using Maximum Parsimony
minimumBranchLen | Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
minimumBranchLength | Scales Edge Lengths of a Phylogeny to a Minimum Branch Length
modelMethods | Model Function Methods: Parameter Names, Bounds and Initial Values
modifyTerminalBranches | Modify, Drop or Bind Terminal Branches of Various Types (Mainly for Paleontological Phylogenies)
multiDiv | Calculating Diversity Curves Across Multiple Datasets

## -- N --

nearestNeighborDist | Nearest Neighbor Distances for Morphological Disparity Studies
nodeDates2branchLengths | Obtaining Edge Lengths for Undated Phylogenies Using Known Branching Node and Tip Ages

## -- O --

obtainDatedPosteriorTreesMrB | Get the Sample of Posterior Trees from a Dated Phylogenetic Analysis with MrBayes (Or a Summary Tree, such as the MCCT)
occData2timeList | Converting Occurrences Data to a 'timeList' Data Object
optimPaleo | Simplified Optimizer for 'paleotree' Likelihood Functions

## -- P --

pairwiseSpearmanRho | Miscellaneous Functions for Community Ecology
paleotree | paleotree: Paleontological and Phylogenetic Analyses of Evolution
parbounds | Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds.constrained | Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds.paleotreeFunc | Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds<- | Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds<-.constrained | Model Function Methods: Parameter Names, Bounds and Initial Values
parbounds<-.paleotreeFunc | Model Function Methods: Parameter Names, Bounds and Initial Values
parentChild2taxonTree | Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table of Parent-Child Taxon Relationships
parInit | Model Function Methods: Parameter Names, Bounds and Initial Values
parInit.constrained | Model Function Methods: Parameter Names, Bounds and Initial Values
parInit.paleotreeFunc | Model Function Methods: Parameter Names, Bounds and Initial Values
parLower | Model Function Methods: Parameter Names, Bounds and Initial Values
parLower.constrained | Model Function Methods: Parameter Names, Bounds and Initial Values
parLower.paleotreeFunc | Model Function Methods: Parameter Names, Bounds and Initial Values
parLower<- | Model Function Methods: Parameter Names, Bounds and Initial Values
parLower<-.constrained | Model Function Methods: Parameter Names, Bounds and Initial Values
parLower<-.paleotreeFunc | Model Function Methods: Parameter Names, Bounds and Initial Values
parnames | Model Function Methods: Parameter Names, Bounds and Initial Values
parnames.constrained | Model Function Methods: Parameter Names, Bounds and Initial Values
parnames.paleotreeFunc | Model Function Methods: Parameter Names, Bounds and Initial Values
parnames<- | Model Function Methods: Parameter Names, Bounds and Initial Values
parnames<-.constrained | Model Function Methods: Parameter Names, Bounds and Initial Values
parnames<-.paleotreeFunc | Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper | Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper.constrained | Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper.paleotreeFunc | Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper<- | Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper<-.constrained | Model Function Methods: Parameter Names, Bounds and Initial Values
parUpper<-.paleotreeFunc | Model Function Methods: Parameter Names, Bounds and Initial Values
perCapitaRates | Instantaneous _per-Capita_ Rates of Origination and Extinction from the Fossil Record
perfectParsCharTree | Simulate a Set of Parsimony-Informative Characters for a Phylogeny
phyloDiv | Diversity Curves
PIE | Miscellaneous Functions for Community Ecology
plotMultiDiv | Calculating Diversity Curves Across Multiple Datasets
plotOccData | Plotting Occurrence Data Across Taxa
plotPhyloPicTree | Plot a Phylogeny with Organismal Silhouettes from PhyloPic, Called Via the Paleobiology Database API
plotTaxaTreePBDB | Creating a Taxon-Tree from Taxonomic Data Downloaded from the Paleobiology Database
plotTraitgram | Plot a Traitgram for Continuous Traits
pqr2Ps | Joint Probability of A Clade Surviving Infinitely or Being Sampled Once
pqsRate2sProb | Converting Sampling Estimates
ProbabilityInterspecificEncounter | Miscellaneous Functions for Community Ecology
probAnc | Probability of being a sampled ancestor of another sampled taxon

## -- Q --

qsProb2Comp | Converting Sampling Estimates
qsRate2Comp | Converting Sampling Estimates

## -- R --

RaiaCopesRule | Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
resolveTreeChar | Resolve Polytomies Using Parsimony-Based Reconstruction of a Discrete Character
retioChar | Cladogram and Range Data for the Retiolitinae
retiolitinae | Cladogram and Range Data for the Retiolitinae
retioRanges | Cladogram and Range Data for the Retiolitinae
retioTree | Cladogram and Range Data for the Retiolitinae
reverseList | Reverse List Structure
rootSplit | Split Tip Taxa by Root Divergence

## -- S --

sampleRanges | Sampling Taxon Ranges
SamplingConv | Converting Sampling Estimates
seqTimeList | Construct a Stochastic Sequenced Time-List from an Unsequenced Time-List
setRootAge | Place a Non-Ultrametric Tree of Fossil Taxa on Absolute Time
setRootAges | Place a Non-Ultrametric Tree of Fossil Taxa on Absolute Time
shellSize | Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015
simCandleTaxa | Simulating Extinct Clades of Monophyletic Taxa
simFossilRecord | Full-Scale Simulations of the Fossil Record with Birth, Death and Sampling of Morphotaxa
simFossilRecordMethods | Methods for Editing or Converting Output from Simulated Fossil Record Objects
simTermTaxa | Simulating Extinct Clades of Monophyletic Taxa
simTermTaxaAdvanced | Simulating Extinct Clades of Monophyletic Taxa
SongZhangDicrano | Cladistic Data for Dicranograptid Graptolites from Song and Zhang (2014)
sProb2sRate | Converting Sampling Estimates
sRate2sProb | Converting Sampling Estimates
sutureComplexity | Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015

## -- T --

taxa2cladogram | Convert Simulated Taxon Data into a Cladogram
taxa2phylo | Convert Simulated Taxon Data into a Phylogeny
taxicDivCont | Diversity Curves
taxicDivDisc | Diversity Curves
taxonSortPBDBocc | Sorting Unique Taxa of a Given Rank from Paleobiology Database Occurrence Data
taxonTable2taxonTree | Create a Taxonomy-Based Phylogeny ('Taxon Tree') from a Hierarchical Table of Taxonomy Memberships
termTaxa | Simulating Extinct Clades of Monophyletic Taxa
testEdgeMat | Test the Edge Matrix of a "phylo" Phylogeny Object for Inconsistencies
timeLadderTree | Resolve Polytomies by Order of First Appearance
timeList2fourDate | Converting Datasets of Taxon Ranges in Intervals Between 'timeList' format and 'fourDate' format
timePaleoPhy | Simplistic _a posteriori_ Dating Approaches For Paleontological Phylogenies
timeSliceFossilRecord | Methods for Editing or Converting Output from Simulated Fossil Record Objects
timeSliceTree | Time-Slicing a Phylogeny
tipdating | Construct a Fully Formatted NEXUS Script for Performing Tip-Dating Analyses With MrBayes
tipDatingCompatabilitySummaryMrB | Get the Compatibility Summary Topology From a Tip-Dating Analysis with MrBayes
treeContradiction | Measure the Contradiction Difference Between Two Phylogenetic Topologies
trueCandle | Simulating Extinct Clades of Monophyletic Taxa
trueTermTaxaTree | Simulating Extinct Clades of Monophyletic Taxa
twoWayEcologyCluster | R-Mode vs Q-Mode Two-Way Cluster Analyses and Abundance Plot for Community Ecology Data

## -- U --

unitLengthTree | Scale Tree to Unit-Length