paleoTS: Analyze Paleontological Time-Series

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.

AuthorGene Hunt
Date of publication2015-12-02 00:08:25
MaintainerGene Hunt <>
LicenseGPL (>= 2)

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Man pages

as.paleoTS: Paleontological time-series class

as.paleoTSfit: Class for fit to paleontological time-series models

bootSimpleComplex: Use parametric bootstrapping to test the fit of a complex...

cat.paleoTS: Miscellaneous functions used internally for punctuations

compareModels: Compare output from any set of model fits

ESD: Compute Expected Squared Divergence (ESD) for simple...

fit3models: Do model fits for standard sets of evolutionary models

fitGpunc: Analyze evolutionary models with unsampled punctuations

fitModeShift: Fit models in which start in Stasis, and then shift to a...

fitMult: Functions to estimate models over multiple time-series

fit.sgs: Analyze evolutionary models with well-sampled punctuations

fitSimple: Fit simple models of trait evolution

IC: Compute information criterion scores and Akaike weights for...

ln.paleoTS: Log transform paleontological time series data

logL.GRW: Compute log-likelihoods for random walk and stasis models

logL.joint.GRW: Log-likelihoods for evolutionary models (joint...

LRI: Log-Rate, Log-Interval (LRI) method of Gingerich

lynchD: Compute rate metric from Lynch (1990)

mle.GRW: Maximum likelihood parameter estimators

modelCurves: Function computes model expectations and 95

opt.covTrack: Covariate-tracking model

opt.GRW: Numerically find maximum likelihood solutions to evolutionary...

opt.GRW.shift: Functions for random walks with shifting parameters

opt.joint.GRW: Optimize evolutionary models (joint parameterization)

paleoTS-package: Analysis of evolutionary time-series

plot.paleoTS: Plots paleoTS objects

sim.covTrack: Simulate time-series that tracks a covariate

sim.GRW: Simulate evolutionary time-series

sim.OU: Simulate evolutionary time-series

sim.punc: Simulate evolutionary time-series with changing dynamics

std.paleoTS: Standardize paleontological time series data

stickleback: Stickleback data from Bell et al. (2006)

sub.paleoTS: Subset an evolutionary time series

test.var.het: Variance heterogeneity test

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