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paleotree (version 2.3)

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

2.3

License

GPL (>= 2)

Issues

Pull Requests

Stars

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Repository

https://github.com/dwbapst/paleotree

Homepage

http://webpages.sdsmt.edu/~dbapst/

Maintainer

David Bapst

Last Published

January 16th, 2015

Functions in paleotree (2.3)

Calculating Diversity Curves Across Multiple Datasets

Convert Simulated Taxon Data into a Phylogeny

getSampRateCont

Fit Models of Sampling Rates to Continuous-Time Taxon Ranges

Simplified Optimizer for paleotree Likelihood Functions

Morphlogical Character and Range Data for late Ordovician and Early Silurian Graptoloidea

Probability of being a sampled ancestor of another sampled taxon

cladogeneticTraitCont

Simulate Cladogenetic Trait Evolution

compareTimescaling

Comparing the Time-Scaling of Trees

Absolute Dates for Nodes of a Time-Scaled Phylogeny

Calculates Values for Foote's Inverse Survivorship Analyses

Paint Tree Branch Depth by Color

paleotree-package

paleotree: Paleontological and Phylogenetic Analyses of Evolution

Plot a Traitgram for Continuous Traits

Time-Slicing a Phylogeny

Joint Probability of A Clade Surviving Infinitely or Being Sampled Once

Bin Simulated Temporal Ranges in Discrete Intervals

Randomly Collapse a Portion of Nodes on a Phylogeny

simFossilTaxa_SRCond

Simulating Taxa in the Fossil Record, Conditioned on Sampling Rate

DiversityCurves

Diversity Curves

getSampProbDisc

Fit Models of Sampling Probability to Discrete-Interval Taxon Ranges

perfectParsCharTree

Simulate a Set of Parsimony-Informative Characters for a Phylogeny

Frequency Ratio Method for Estimating Sampling Probability

Partitions the branch lengths of a tree into several classes based on their placement.

Simulating Un-Conditioned Trees of Fossil Taxa

cal3TimePaleoPhy

Three Rate Calibrated Timescaling of Paleo-Phylogenies

Timescaling of Paleo-Phylogenies

nearestNeighborDist

Nearest Neighbor Distances for Morphological Disparity Studies

minBranchLength

Scales Edge Lengths of a Phylogeny to a Minimum Branch Length

constrainParPaleo

Constrain Parameters for a Model Function from paleotree

Scale Tree to Unit-Length

Model Function Methods: Parameter Names, Bounds and Initial Values

expandTaxonTree

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

Construct a Stochastic Sequenced Time-List from an Unsequenced Time-List

Sampling Taxon Ranges

Resolve Polytomies by Order of First Appearance

Convert Simulated Taxon Data into a Cladogram

Cladogram and Range Data for the Retiolitinae

Split Tip Taxa by Root Divergence

modifyTerminalBranches

Modify or Drop Terminal Branches of Various Types

horizonSampRate

Estimate Sampling Rate from Sampling Horizon Data (Solow and Smith, 1997)

Models of Sampling and Extinction for Taxonomic Duration Datasets

Inverse Survivorship Models in the Fossil Record

Converting Sampling Estimates

Reverse List Structure

Simulating Taxa in the Fossil Record

Simulating Extinct Clades of Monophyletic Taxa