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paleotree (version 1.5)

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

1.5

License

GPL (>= 2)

Maintainer

David Bapst

Last Published

October 6th, 2012

Functions in paleotree (1.5)

Bin Temporal Ranges in Discrete Intervals

getSampRateCont

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges

Plot a Traitgram for Continuous Traits

getSampProbDisc

Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges

expandTaxonTree

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

cal3Timescaling

Three Rate Calibrated Timescaling of Paleo-Phylogenies

Convert Simulated Taxon Data into a Cladogram

Resolve Polytomies by Order of First Appearance

Paint Tree Branch Depth by Color

Convert Simulated Taxon Data into a Phylogeny

Simulating Un-Conditioned Trees of Fossil Taxa

Sampling Taxon Ranges

SampRate-Calibrated Timescaling of Paleo-Phylogenies

Reverse List Structure

Converting Sampling Estimates

Timescaling of Paleo-Phylogenies

cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution

Calculating Diversity Curves Across Multiple Datasets

paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution

Frequency Ratio Method for Estimating Sampling Probability

Simulating Taxa in the Fossil Record

Scale Tree to Unit-Length

Randomly collapse nodes on a phylogeny

DiversityCurves

Diversity Curves

compareTimescaling

Comparing the Time-Scaling of Trees

modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types

Split Tip Taxa by Root Divergence

Time-Slicing a Phylogeny