Man pages for paleotree
Paleontological and Phylogenetic Analyses of Evolution

binTimeDataBin Simulated Temporal Ranges in Discrete Intervals
branchClassesPartitions the branch lengths of a tree into several classes...
cal3TimePaleoPhyThree Rate Calibrated 'a posteriori' Time-Scaling of...
cladogeneticTraitContSimulate Cladogenetic Trait Evolution
communityEcologyMiscellaneous Functions for Community Ecology
compareTimescalingComparing the Time-Scaling of Trees
constrainParPaleoConstrain Parameters for a Model Function from paleotree
createMrBayesConstraintsTransform a Topology into a Set of Constraint Commands for...
createMrBayesTipCalibrationsConstruct A Block of Tip Age Calibrations for Use with...
createMrBayesTipDatingNexusConstruct a Fully Formatted NEXUS Script for Performing...
dateNodesAbsolute Dates for Nodes of a Time-Scaled Phylogeny
degradeTreeRandomly Collapse a Portion of Nodes on a Phylogeny
depthRainbowPaint Tree Branch Depth by Color
divCurveFossilRecordSimDiversity-Curve Plotting for Simulations of Diversification...
DiversityCurvesDiversity Curves
durationFreqModels of Sampling and Extinction for Taxonomic Duration...
equation2functionTurn a Character String of the Right-Hand Side of an Equation...
exhaustionFunctionsAnalyses of the exhaustion of Character States Over...
expandTaxonTreeExtrapolating Lower-Level Taxon Phylogenies from Higher-Level...
footeValuesCalculates Values for Foote's Inverse Survivorship Analyses
freqRatFrequency Ratio Method for Estimating Sampling Probability
graptDisparityMorphlogical Character and Range Data for late Ordovician and...
graptPBDBExample Occurrence and Taxonomic Datasets of the...
horizonSampRateEstimate Sampling Rate from Sampling Horizon Data (Solow and...
inverseSurvInverse Survivorship Models in the Fossil Record
kantoExample Species Abundances Tables
macroperforateForamAncestor-Descendant Relationships for Macroperforate...
makePBDBtaxonTreeCreating a Taxon-Tree from Taxonomic Data Downloaded from the...
minBranchLengthScales Edge Lengths of a Phylogeny to a Minimum Branch Length
minCharChangeEstimating the Minimum Number of Character Transitions Using...
modelMethodsModel Function Methods: Parameter Names, Bounds and Initial...
modifyTerminalBranchesModify, Drop or Bind Terminal Branches of Various Types...
multiDivCalculating Diversity Curves Across Multiple Datasets
nearestNeighborDistNearest Neighbor Distances for Morphological Disparity...
nodeDates2branchLengthsObtaining Edge Lengths for Undated Phylogenies Using Known...
obtainDatedPosteriorTreesMrBGet the Sample of Posterior Trees from a Dated Phylogenetic...
occData2timeListConverting Occurrences Data to a timeList Data Object
optimPaleoSimplified Optimizer for paleotree Likelihood Functions
paleotree-packagepaleotree: Paleontological and Phylogenetic Analyses of...
parentChild2taxonTreeCreate a Taxonomy-Based Phylogeny ('Taxon Tree') from a Table...
perCapitaRatesperCapitaRates
perfectParsCharTreeSimulate a Set of Parsimony-Informative Characters for a...
plotOccDataPlotting Occurrence Data Across Taxa
plotTraitgramPlot a Traitgram for Continuous Traits
pqr2PsJoint Probability of A Clade Surviving Infinitely or Being...
probAncProbability of being a sampled ancestor of another sampled...
RaiaCopesRuleDated Trees and Trait Data for Ammonites, Ceratopsians and...
resolveTreeCharResolve Polytomies Using Parsimony-Based Reconstruction of a...
retiolitinaeCladogram and Range Data for the Retiolitinae
reverseListReverse List Structure
rootSplitSplit Tip Taxa by Root Divergence
sampleRangesSampling Taxon Ranges
SamplingConvConverting Sampling Estimates
seqTimeListConstruct a Stochastic Sequenced Time-List from an...
setRootAgePlace a Non-Ultrametric Tree of Fossil Taxa on Absolute Time
simFossilRecordFull-Scale Simulations of the Fossil Record with Birth, Death...
simFossilRecordMethodsMethods for Editing or Converting Output from simFossilRecord
SongZhangDicranoCladistic Data for Dicranograptid Graptolites from Song and...
taxa2cladogramConvert Simulated Taxon Data into a Cladogram
taxa2phyloConvert Simulated Taxon Data into a Phylogeny
taxonSortPBDBoccSorting Unique Taxa of a Given Rank from Paleobiology...
taxonTable2taxonTreeCreate a Taxonomy-Based Phylogeny ('Taxon Tree') from a...
termTaxaSimulating Extinct Clades of Monophyletic Taxa
testEdgeMatTest the Edge Matrix of a 'phylo' Phylogeny Object for...
timeLadderTreeResolve Polytomies by Order of First Appearance
timeList2fourDateConverting Datasets of Taxon Ranges in Intervals Between...
timePaleoPhyTypical 'a posteriori' Time-Scaling Approaches For...
timeSliceTreeTime-Slicing a Phylogeny
treeContradictionMeasure the Contradiction Difference Between Two Phylogenetic...
unitLengthTreeScale Tree to Unit-Length
paleotree documentation built on July 10, 2018, 1:06 a.m.