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paleotree (version 1.9)

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

1.9

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

January 3rd, 2014

Functions in paleotree (1.9)

expandTaxonTree

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

Diversity Curves
retiolitinae

Cladogram and Range Data for the Retiolitinae
taxa2phylo

Convert Simulated Taxon Data into a Phylogeny
modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types
rootSplit

Split Tip Taxa by Root Divergence
reverseList

Reverse List Structure
timePaleoPhy

Timescaling of Paleo-Phylogenies
cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution
footeValues

Calculates Values for Foote's Inverse Survivorship Analyses
depthRainbow

Paint Tree Branch Depth by Color
pqr2Ps

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

Probability of being a sampled ancestor of another sampled taxon
binTimeData

Bin Simulated Temporal Ranges in Discrete Intervals
freqRat

Frequency Ratio Method for Estimating Sampling Probability
simPaleoTrees

Simulating Un-Conditioned Trees of Fossil Taxa
taxa2cladogram

Convert Simulated Taxon Data into a Cladogram
perCapitaRates

perCapitaRates
getSampProbDisc

Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges
paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution
cal3TimePaleoPhy

Three Rate Calibrated Timescaling of Paleo-Phylogenies
horizonSampRate

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

Converting Sampling Estimates
multiDiv

Calculating Diversity Curves Across Multiple Datasets
degradeTree

Randomly Collapse a Portion of Nodes on a Phylogeny
durationFreq

Models of Sampling and Extinction for Taxonomic Duration Datasets
optimPaleo

Simplified Optimizer for paleotree Likelihood Functions
simFossilTaxa

Simulating Taxa in the Fossil Record
unitLengthTree

Scale Tree to Unit-Length
termTaxa

Simulating Extinct Clades of Monophyletic Taxa
constrainParPaleo

Constrain Parameters for a Model Function from paleotree
sampleRanges

Sampling Taxon Ranges
simFossilTaxa_SRCond

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

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

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

Resolve Polytomies by Order of First Appearance
plotTraitgram

Plot a Traitgram for Continuous Traits
branchClasses

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

Comparing the Time-Scaling of Trees
timeSliceTree

Time-Slicing a Phylogeny