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paleoTS (version 0.5-1)

Analyze Paleontological Time-Series

Description

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

0.5-1

License

GPL (>= 2)

Maintainer

Gene Hunt

Last Published

December 2nd, 2015

Functions in paleoTS (0.5-1)

Fit simple models of trait evolution

Analyze evolutionary models with unsampled punctuations

Simulate evolutionary time-series with changing dynamics

Simulate evolutionary time-series

Miscellaneous functions used internally for punctuations

Do model fits for standard sets of evolutionary models

Fit models in which start in Stasis, and then shift to a random walk (or vice versa)

bootSimpleComplex

Use parametric bootstrapping to test the fit of a complex model relative to a simpler one

Optimize evolutionary models (joint parameterization)

Compute information criterion scores and Akaike weights for evoltuionary models

Compute rate metric from Lynch (1990)

Compute log-likelihoods for random walk and stasis models

Analyze evolutionary models with well-sampled punctuations

Compute Expected Squared Divergence (ESD) for simple evolutionary models

Function computes model expectations and 95

Log-likelihoods for evolutionary models (joint parameterization)

Class for fit to paleontological time-series models

Plots paleoTS objects

Log transform paleontological time series data

Numerically find maximum likelihood solutions to evolutionary models

Compare output from any set of model fits

Stickleback data

Stickleback data from Bell et al. (2006)

Paleontological time-series class

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

Subset an evolutionary time series

Covariate-tracking model

Maximum likelihood parameter estimators

Variance heterogeneity test

paleoTS-package

Analysis of evolutionary time-series

Functions for random walks with shifting parameters

Simulate time-series that tracks a covariate

Standardize paleontological time series data

Simulate evolutionary time-series

Functions to estimate models over multiple time-series