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paleotree (version 2.1)

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

2.1

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

August 16th, 2014

Functions in paleotree (2.1)

horizonSampRate

Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 1997)
cal3TimePaleoPhy

Three Rate Calibrated Timescaling of Paleo-Phylogenies
footeValues

Calculates Values for Foote's Inverse Survivorship Analyses
depthRainbow

Paint Tree Branch Depth by Color
cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution
expandTaxonTree

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

Diversity Curves
SamplingConv

Converting Sampling Estimates
inverseSurv

Inverse Survivorship Models in the Fossil Record
taxa2cladogram

Convert Simulated Taxon Data into a Cladogram
multiDiv

Calculating Diversity Curves Across Multiple Datasets
reverseList

Reverse List Structure
timeLadderTree

Resolve Polytomies by Order of First Appearance
simFossilTaxa_SRCond

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

Modify or Drop Terminal Branches of Various Types
unitLengthTree

Scale Tree to Unit-Length
durationFreq

Models of Sampling and Extinction for Taxonomic Duration Datasets
perfectParsCharTree

Simulate a Set of Parsimony-Informative Characters for a Phylogeny
simPaleoTrees

Simulating Un-Conditioned Trees of Fossil Taxa
taxa2phylo

Convert Simulated Taxon Data into a Phylogeny
plotTraitgram

Plot a Traitgram for Continuous Traits
pqr2Ps

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

Cladogram and Range Data for the Retiolitinae
getSampRateCont

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

Randomly Collapse a Portion of Nodes on a Phylogeny
termTaxa

Simulating Extinct Clades of Monophyletic Taxa
branchClasses

Partitions the branch lengths of a tree into several classes based on their placement.
paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution
constrainParPaleo

Constrain Parameters for a Model Function from paleotree
modelMethods

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

Simulating Taxa in the Fossil Record
compareTimescaling

Comparing the Time-Scaling of Trees
sampleRanges

Sampling Taxon Ranges
timePaleoPhy

Timescaling of Paleo-Phylogenies
optimPaleo

Simplified Optimizer for paleotree Likelihood Functions
binTimeData

Bin Simulated Temporal Ranges in Discrete Intervals
dateNodes

Absolute Dates for Nodes of a Time-Scaled Phylogeny
perCapitaRates

perCapitaRates
timeSliceTree

Time-Slicing a Phylogeny
getSampProbDisc

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

Frequency Ratio Method for Estimating Sampling Probability
rootSplit

Split Tip Taxa by Root Divergence
seqTimeList

Construct a Stochastic Sequenced Time-List from an Unsequenced Time-List
probAnc

Probability of being a sampled ancestor of another sampled taxon