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paleotree (version 1.0)

Analyses for Paleontological Phylogenies

Description

Analyzes, time-scales and simulates phylogenies of extinct/fossil lineages. Also plots diversity curves for stratigraphic range data and phylogenies, including combinations of the those two data types.

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Version

Install

install.packages('paleotree')

Monthly Downloads

837

Version

1.0

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

January 27th, 2012

Functions in paleotree (1.0)

timePaleoPhy

Timescaling of Paleo-Phylogenies

ConvSampEst

Converting Sampling Estimates

depthRainbow

Paint Tree Depth by Color

srcTimescaling

SampRate-Calibrated Timescaling of Paleo-Phylogenies

taxa2cladogram

Converting taxon data into cladogram

DiversityCurves

Diversity Curves

degradeTree

Randomly collapse nodes on a phylogeny

getSampProbDisc

Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges

expandTaxonTree

Extrapolating Lower Taxon Phylogenies from Higher Taxon Trees

taxa2phylo

Convert taxon data into Phylogeny

timeSliceTree

Taking a Timeslice of a Tree

dropZLB

Drop Terminal Zero-Length Branches

multiDiv

Calculating Diversity Curves Across Multiple Datasets

getSampRateCont

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges

simFossilTaxa

Simulating Taxa in the Fossil Record

unitLengthTree

Scale Tree to Unit-Length

sampleRanges

Sampling Taxon Ranges

paleotree-package

paleotree: Analyses for Paleontological Phylogenies

plotTraitgram

Plot a Traitgram for Continuous Traits

simPaleoTrees

Simulating Un-Conditioned Trees of Fossil Taxa

binTimeData

Bin Temporal Ranges in Discrete Intervals