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paleotree (version 1.6)

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

1.6

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

November 6th, 2012

Functions in paleotree (1.6)

Timescaling of Paleo-Phylogenies

Scale Tree to Unit-Length

Simulating Extinct Clades of Monophyletic Taxa

Sampling Taxon Ranges

getSampProbDisc

Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges

Paint Tree Branch Depth by Color

cal3Timescaling

Three Rate Calibrated Timescaling of Paleo-Phylogenies

paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution

Simulating Taxa in the Fossil Record

Convert Simulated Taxon Data into a Phylogeny

Time-Slicing a Phylogeny

expandTaxonTree

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

Calculating Diversity Curves Across Multiple Datasets

Randomly collapse nodes on a phylogeny

compareTimescaling

Comparing the Time-Scaling of Trees

Simulating Un-Conditioned Trees of Fossil Taxa

Reverse List Structure

DiversityCurves

Diversity Curves

Resolve Polytomies by Order of First Appearance

modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types

Convert Simulated Taxon Data into a Cladogram

Frequency Ratio Method for Estimating Sampling Probability

Plot a Traitgram for Continuous Traits

Split Tip Taxa by Root Divergence

Bin Temporal Ranges in Discrete Intervals

getSampRateCont

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges

Converting Sampling Estimates

cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution