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paleotree (version 2.0)

Paleontological and Phylogenetic Analyses of Evolution

Description

Analyzes, time-scales and simulates phylogenies of extinct/fossil lineages, along with calculation of diversity curves. Also fits likelihood models to estimate sampling rates from stratigraphic ranges.

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Version

Install

install.packages('paleotree')

Monthly Downloads

980

Version

2.0

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

February 4th, 2014

Functions in paleotree (2.0)

constrainParPaleo

Constrain Parameters for a Model Function from paleotree
optimPaleo

Simplified Optimizer for paleotree Likelihood Functions
taxa2cladogram

Convert Simulated Taxon Data into a Cladogram
modelMethods

Model Function Methods: Parameter Names, Bounds and Initial Values
SamplingConv

Converting Sampling Estimates
expandTaxonTree

Extrapolating Lower-Level Taxon Phylogenies from Higher-Level Taxon Trees
branchClasses

Partitions the branch lengths of a tree into several classes based on their placement.
horizonSampRate

Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 1997)
freqRat

Frequency Ratio Method for Estimating Sampling Probability
cal3TimePaleoPhy

Three Rate Calibrated Timescaling of Paleo-Phylogenies
DiversityCurves

Diversity Curves
depthRainbow

Paint Tree Branch Depth by Color
inverseSurv

Inverse Survivorship Models in the Fossil Record
reverseList

Reverse List Structure
timeLadderTree

Resolve Polytomies by Order of First Appearance
taxa2phylo

Convert Simulated Taxon Data into a Phylogeny
timeSliceTree

Time-Slicing a Phylogeny
modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types
simFossilTaxa

Simulating Taxa in the Fossil Record
durationFreq

Models of Sampling and Extinction for Taxonomic Duration Datasets
plotTraitgram

Plot a Traitgram for Continuous Traits
degradeTree

Randomly Collapse a Portion of Nodes on a Phylogeny
compareTimescaling

Comparing the Time-Scaling of Trees
paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution
probAnc

Probability of being a sampled ancestor of another sampled taxon
footeValues

Calculates Values for Foote's Inverse Survivorship Analyses
multiDiv

Calculating Diversity Curves Across Multiple Datasets
pqr2Ps

Joint Probability of A Clade Surviving Infinitely or Being Sampled Once
perCapitaRates

perCapitaRates
timePaleoPhy

Timescaling of Paleo-Phylogenies
sampleRanges

Sampling Taxon Ranges
rootSplit

Split Tip Taxa by Root Divergence
binTimeData

Bin Simulated Temporal Ranges in Discrete Intervals
simPaleoTrees

Simulating Un-Conditioned Trees of Fossil Taxa
termTaxa

Simulating Extinct Clades of Monophyletic Taxa
cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution
getSampProbDisc

Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges
retiolitinae

Cladogram and Range Data for the Retiolitinae
dateNodes

Absolute Dates for Nodes of a Time-Scaled Phylogeny
getSampRateCont

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges
simFossilTaxa_SRCond

Simulating Taxa in the Fossil Record, Conditioned on Sampling Rate
unitLengthTree

Scale Tree to Unit-Length