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paleotree (version 1.4)

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

1.4

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

June 18th, 2012

Functions in paleotree (1.4)

DiversityCurves

Diversity Curves

degradeTree

Randomly collapse nodes on a phylogeny

taxa2cladogram

Convert Simulated Taxon Data into a Cladogram

timePaleoPhy

Timescaling of Paleo-Phylogenies

modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types

plotTraitgram

Plot a Traitgram for Continuous Traits

expandTaxonTree

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

unitLengthTree

Scale Tree to Unit-Length

compareTimescaling

Comparing the Time-Scaling of Trees

multiDiv

Calculating Diversity Curves Across Multiple Datasets

depthRainbow

Paint Tree Branch Depth by Color

getSampProbDisc

Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges

srcTimescaling

SampRate-Calibrated Timescaling of Paleo-Phylogenies

taxa2phylo

Convert Simulated Taxon Data into a Phylogeny

simFossilTaxa

Simulating Taxa in the Fossil Record

timeSliceTree

Time-Slicing a Phylogeny

paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution

simPaleoTrees

Simulating Un-Conditioned Trees of Fossil Taxa

sampleRanges

Sampling Taxon Ranges

cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution

SamplingConv

Converting Sampling Estimates

binTimeData

Bin Temporal Ranges in Discrete Intervals

getSampRateCont

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges