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paleotree (version 1.8.2)

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

841

Version

1.8.2

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

September 4th, 2013

Functions in paleotree (1.8.2)

rootSplit

Split Tip Taxa by Root Divergence
timeLadderTree

Resolve Polytomies by Order of First Appearance
timeSliceTree

Time-Slicing a Phylogeny
simPaleoTrees

Simulating Un-Conditioned Trees of Fossil Taxa
expandTaxonTree

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

Calculating Diversity Curves Across Multiple Datasets
sampleRanges

Sampling Taxon Ranges
SamplingConv

Converting Sampling Estimates
cal3Timescaling

Three Rate Calibrated Timescaling of Paleo-Phylogenies
paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution
retiolitinae

Cladogram and Range Data for the Retiolitinae
binTimeData

Bin Temporal Ranges in Discrete Intervals
compareTimescaling

Comparing the Time-Scaling of Trees
termTaxa

Simulating Extinct Clades of Monophyletic Taxa
timePaleoPhy

Timescaling of Paleo-Phylogenies
taxa2phylo

Convert Simulated Taxon Data into a Phylogeny
degradeTree

Randomly collapse nodes on a phylogeny
freqRat

Frequency Ratio Method for Estimating Sampling Probability
depthRainbow

Paint Tree Branch Depth by Color
getSampRateCont

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

Reverse List Structure
getSampProbDisc

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

Plot a Traitgram for Continuous Traits
modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types
simFossilTaxa

Simulating Taxa in the Fossil Record
taxa2cladogram

Convert Simulated Taxon Data into a Cladogram
DiversityCurves

Diversity Curves
cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution
unitLengthTree

Scale Tree to Unit-Length
simFossilTaxa_SRCond

Simulating Taxa in the Fossil Record, Conditioned on Sampling Rate