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paleoTS (version 0.3-1)

Modeling evolution in 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, and Ornstein-Uhlenbeck models. Newly added to this version (0.3-1) are functions to analyze punctuations and models in which evolutionary dynamics change over the course of a time-series of trait values.

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Version

Install

install.packages('paleoTS')

Monthly Downloads

460

Version

0.3-1

License

GPL (>= 2)

Maintainer

Gene Hunt

Last Published

September 10th, 2024

Functions in paleoTS (0.3-1)

fit.sgs

Analyze evolutionary models with well-sampled punctuations
sim.OU

Simulate evolutionary time-series
sim.punc

Simulate evolutionary time-series with changing dynamics
fitGpunc

Analyze evolutionary models with unsampled punctuations
lynchD

Compute rate metric from Lynch (1990)
logL.GRW

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

Numerically find maximum likelihood solutions to evolutionary models
test.var.het

Variance heterogeneity test
IC

Compute information criterion scores and Akaike weights for evoltuionary models
mle.GRW

Maximum likelihood parameter estimators
Stickleback data

Stickleback data from Bell et al. (2006)
sub.paleoTS

Subset an evolutionary time series
fit3models

Do model fits for three standard evolutionary models
cat.paleoTS

Miscellaneous functions used internally for punctuations
opt.GRW.shift

Functions for random walks with shifting parameters
opt.RW.Mult

Functions to analyze multiple time-series jointly
as.paleoTS

Paleontological time-series class
ln.paleoTS

Log transform paleontological time series data
opt.joint.GRW

Optimize evolutionary models (joint parameterization)
plot.paleoTS

Plots paleoTS objects
paleoTS-package

Analysis of evoltuionary time-series
logL.joint.GRW

Log-likelihoods for evolutionary models (joint parameterization)
std.paleoTS

Standardize paleontological time series data
add.OU.curves

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

Simulate evolutionary time-series