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.

Install the latest version of this package by entering the following in R:
install.packages("paleoTS")
AuthorGene Hunt
Date of publication2015-12-02 00:08:25
MaintainerGene Hunt <hunte@si.edu>
LicenseGPL (>= 2)
Version0.5-1

View on CRAN

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

Functions

akaike.wts Man page
as.paleoTS Man page
as.paleoTSfit Man page
bootSimpleComplex Man page
cat.paleoTS Man page
compareModels Man page
dorsal.spines Man page
ESD Man page
fit3models Man page
fit4models Man page
fit9models Man page
fitGpunc Man page
fitModeShift Man page
fitMult Man page
fit.sgs Man page
fitSimple Man page
IC Man page
ln.paleoTS Man page
logL.covTrack Man page
logL.GRW Man page
logL.joint.covTrack Man page
logL.joint.GRW Man page
logL.joint.GRW.Stasis Man page
logL.joint.Mult Man page
logL.joint.OU Man page
logL.joint.punc Man page
logL.joint.punc.omega Man page
logL.joint.Stasis Man page
logL.joint.Stasis.GRW Man page
logL.joint.Stasis.URW Man page
logL.joint.StrictStasis Man page
logL.joint.URW Man page
logL.joint.URW.Stasis Man page
logL.Mult Man page
logL.Mult.covTrack Man page
logL.Mult.joint.covTrack Man page
logL.punc Man page
logL.punc.omega Man page
logL.SameMs Man page
logL.SameVs Man page
logL.sgs Man page
logL.sgs.omega Man page
logL.Stasis Man page
logL.StrictStasis Man page
logL.URW Man page
LRI Man page
lynchD Man page
mle.GRW Man page
mle.Stasis Man page
mle.URW Man page
modelCurves Man page
opt.AD.RW.Stasis Man page
opt.AD.Stasis.RW Man page
opt.covTrack Man page
opt.covTrack.Mult Man page
opt.GRW Man page
opt.GRW.shift Man page
opt.joint.covTrack Man page
opt.joint.covTrack.Mult Man page
opt.joint.GRW Man page
opt.joint.Mult Man page
opt.joint.OU Man page
opt.joint.punc Man page
opt.joint.RW.Stasis Man page
opt.joint.Stasis Man page
opt.joint.Stasis.RW Man page
opt.joint.StrictStasis Man page
opt.joint.URW Man page
opt.Mult Man page
opt.punc Man page
opt.RW.SameMs Man page
opt.RW.SameVs Man page
opt.sgs Man page
opt.Stasis Man page
opt.StrictStasis Man page
opt.URW Man page
ou.M Man page
ou.V Man page
paleoTS Man page
paleoTS-package Man page
pelvic.score Man page
plot.paleoTS Man page
pool.var Man page
pterygiophores Man page
read.paleoTS Man page
shift2gg Man page
shifts Man page
sim.covTrack Man page
sim.GRW Man page
sim.GRW.shift Man page
sim.OU Man page
sim.punc Man page
sim.sgs Man page
sim.Stasis Man page
split4punc Man page
std.paleoTS Man page
sub.paleoTS Man page
test.var.het Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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