DiversityCurves         Diversity Curves
RaiaCopesRule           Dated Trees and Trait Data for Ammonites,
                        Ceratopsians and Cervids from Raia et al. 2015
SamplingConv            Converting Sampling Estimates
SongZhangDicrano        Cladistic Data for Dicranograptid Graptolites
                        from Song and Zhang (2014)
binTimeData             Bin Simulated Temporal Ranges in Discrete
                        Intervals
branchClasses           Partitions the branch lengths of a tree into
                        several classes based on their placement.
cal3TimePaleoPhy        Three Rate Calibrated _a posteriori_ Dating of
                        Paleontological Phylogenies
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 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
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
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
durationFreq            Models of Sampling and Extinction for Taxonomic
                        Duration Datasets
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
fixRootTime             Modify, Drop or Bind Terminal Branches of
                        Various Types (Mainly for Paleontological
                        Phylogenies)
footeValues             Calculates Values for Foote's Inverse
                        Survivorship Analyses
freqRat                 Frequency Ratio Method for Estimating Sampling
                        Probability
getDataPBDB             Obtaining Data for Taxa or Occurrences From
                        Paleobiology Database API
graptDisparity          Morphlogical Character and Range Data for late
                        Ordovician and Early Silurian Graptoloidea
graptPBDB               Example Occurrence and Taxonomic Datasets of
                        the Graptolithina from the Paleobiology
                        Database
horizonSampRate         Estimate Sampling Rate from Sampling Horizon
                        Data (Solow and Smith, 1997)
inverseSurv             Inverse Survivorship Models in the Fossil
                        Record
kanto                   Example Species Abundances Tables
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
minBranchLength         Scales Edge Lengths of a Phylogeny to a Minimum
                        Branch Length
minCharChange           Estimating the Minimum Number of Character
                        Transitions Using Maximum Parsimony
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
nearestNeighborDist     Nearest Neighbor Distances for Morphological
                        Disparity Studies
nodeDates2branchLengths
                        Obtaining Edge Lengths for Undated Phylogenies
                        Using Known Branching Node and Tip Ages
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
paleotree-package       paleotree: Paleontological and Phylogenetic
                        Analyses of Evolution
parentChild2taxonTree   Create a Taxonomy-Based Phylogeny ('Taxon
                        Tree') from a Table of Parent-Child Taxon
                        Relationships
perCapitaRates          Instantaneous _per-Capita_ Rates of Origination
                        and Extinction from the Fossil Record
perfectParsCharTree     Simulate a Set of Parsimony-Informative
                        Characters for a Phylogeny
plotOccData             Plotting Occurrence Data Across Taxa
plotPhyloPicTree        Plot a Phylogeny with Organismal Silhouettes
                        from PhyloPic, Called Via the Paleobiology
                        Database API
plotTraitgram           Plot a Traitgram for Continuous Traits
pqr2Ps                  Joint Probability of A Clade Surviving
                        Infinitely or Being Sampled Once
probAnc                 Probability of being a sampled ancestor of
                        another sampled taxon
resolveTreeChar         Resolve Polytomies Using Parsimony-Based
                        Reconstruction of a Discrete Character
retiolitinae            Cladogram and Range Data for the Retiolitinae
reverseList             Reverse List Structure
rootSplit               Split Tip Taxa by Root Divergence
sampleRanges            Sampling Taxon Ranges
seqTimeList             Construct a Stochastic Sequenced Time-List from
                        an Unsequenced Time-List
setRootAge              Place a Non-Ultrametric Tree of Fossil Taxa on
                        Absolute Time
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
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 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
timeSliceTree           Time-Slicing a Phylogeny
tipDatingCompatabilitySummaryMrB
                        Get the Compatibility Summary Topology From a
                        Tip-Dating Analysis with MrBayes
treeContradiction       Measure the Contradiction Difference Between
                        Two Phylogenetic Topologies
twoWayEcologyCluster    R-Mode vs Q-Mode Two-Way Cluster Analyses and
                        Abundance Plot for Community Ecology Data
unitLengthTree          Scale Tree to Unit-Length
