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paleoTS (version 0.4-1)

Analyze paleontological time-series

Description

This package facilitates analysis of paleontological sequences of trait values from an evolving lineage. Functions are provided to fit, using maximum likelihood, evolutionary models including unbiased random walks, directional evolution, stasis, Ornstein-Uhlenbeck, punctuated change, and evolutionary models in which traits track some measured covariate.

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Version

Install

install.packages('paleoTS')

Monthly Downloads

460

Version

0.4-1

License

GPL (>= 2)

Maintainer

Gene Hunt

Last Published

March 15th, 2011

Functions in paleoTS (0.4-1)

LRI

Log-Rate, Log-Interval (LRI) method of Gingerich
cat.paleoTS

Miscellaneous functions used internally for punctuations
Stickleback data

Stickleback data from Bell et al. (2006)
fit.sgs

Analyze evolutionary models with well-sampled punctuations
paleoTS-package

Analysis of evoltuionary time-series
mle.GRW

Maximum likelihood parameter estimators
paleoTS-internal

Internal paleoTS objects
as.paleoTS

Paleontological time-series class
fit3models

Do model fits for three standard evolutionary models
opt.joint.GRW

Optimize evolutionary models (joint parameterization)
logL.GRW

Compute log-likelihoods for random walk and stasis models
opt.RW.Mult

Functions to analyze multiple time-series jointly
logL.joint.GRW

Log-likelihoods for evolutionary models (joint parameterization)
sim.covTrack

Simulate time-series that tracks a covariate
sim.punc

Simulate evolutionary time-series with changing dynamics
sim.OU

Simulate evolutionary time-series
fitGpunc

Analyze evolutionary models with unsampled punctuations
IC

Compute information criterion scores and Akaike weights for evoltuionary models
add.OU.curves

Adds curves to an existing plot indicating best-fit OU model
opt.GRW

Numerically find maximum likelihood solutions to evolutionary models
ln.paleoTS

Log transform paleontological time series data
lynchD

Compute rate metric from Lynch (1990)
plot.paleoTS

Plots paleoTS objects
test.var.het

Variance heterogeneity test
compareModels

Compare output from any set of model fits
sim.GRW

Simulate evolutionary time-series
std.paleoTS

Standardize paleontological time series data
opt.covTrack

Covariate-tracking model
as.paleoTSfit

Class for fit to paleontological time-series models
opt.GRW.shift

Functions for random walks with shifting parameters
sub.paleoTS

Subset an evolutionary time series