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paleotree (version 1.7)

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

1.7

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

December 31st, 2012

Functions in paleotree (1.7)

timeLadderTree

Resolve Polytomies by Order of First Appearance
SamplingConv

Converting Sampling Estimates
termTaxa

Simulating Extinct Clades of Monophyletic Taxa
simFossilTaxa_SRCond

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

Scale Tree to Unit-Length
simPaleoTrees

Simulating Un-Conditioned Trees of Fossil Taxa
freqRat

Frequency Ratio Method for Estimating Sampling Probability
expandTaxonTree

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

Reverse List Structure
simFossilTaxa

Simulating Taxa in the Fossil Record
depthRainbow

Paint Tree Branch Depth by Color
timePaleoPhy

Timescaling of Paleo-Phylogenies
sampleRanges

Sampling Taxon Ranges
binTimeData

Bin Temporal Ranges in Discrete Intervals
timeSliceTree

Time-Slicing a Phylogeny
paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution
taxa2phylo

Convert Simulated Taxon Data into a Phylogeny
plotTraitgram

Plot a Traitgram for Continuous Traits
multiDiv

Calculating Diversity Curves Across Multiple Datasets
modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types
degradeTree

Randomly collapse nodes on a phylogeny
getSampProbDisc

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

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges
taxa2cladogram

Convert Simulated Taxon Data into a Cladogram
DiversityCurves

Diversity Curves
compareTimescaling

Comparing the Time-Scaling of Trees
rootSplit

Split Tip Taxa by Root Divergence
cal3Timescaling

Three Rate Calibrated Timescaling of Paleo-Phylogenies
cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution