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paleotree (version 1.8.1)

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

1.8.1

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

April 4th, 2013

Functions in paleotree (1.8.1)

cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution
multiDiv

Calculating Diversity Curves Across Multiple Datasets
getSampRateCont

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

Scale Tree to Unit-Length
SamplingConv

Converting Sampling Estimates
depthRainbow

Paint Tree Branch Depth by Color
simFossilTaxa_SRCond

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

Sampling Taxon Ranges
DiversityCurves

Diversity Curves
timeLadderTree

Resolve Polytomies by Order of First Appearance
taxa2phylo

Convert Simulated Taxon Data into a Phylogeny
timePaleoPhy

Timescaling of Paleo-Phylogenies
timeSliceTree

Time-Slicing a Phylogeny
compareTimescaling

Comparing the Time-Scaling of Trees
reverseList

Reverse List Structure
getSampProbDisc

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

Simulating Extinct Clades of Monophyletic Taxa
cal3Timescaling

Three Rate Calibrated Timescaling of Paleo-Phylogenies
plotTraitgram

Plot a Traitgram for Continuous Traits
expandTaxonTree

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

Simulating Taxa in the Fossil Record
rootSplit

Split Tip Taxa by Root Divergence
binTimeData

Bin Temporal Ranges in Discrete Intervals
paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution
simPaleoTrees

Simulating Un-Conditioned Trees of Fossil Taxa
degradeTree

Randomly collapse nodes on a phylogeny
modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types
freqRat

Frequency Ratio Method for Estimating Sampling Probability
taxa2cladogram

Convert Simulated Taxon Data into a Cladogram
retiolitinae

Cladogram and Range Data for the Retiolitinae