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.

Author
Gene Hunt
Date of publication
2015-12-02 00:08:25
Maintainer
Gene Hunt <hunte@si.edu>
License
GPL (>= 2)
Version
0.5-1

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

Files in this package

paleoTS
paleoTS/NAMESPACE
paleoTS/data
paleoTS/data/dorsal.spines.rda
paleoTS/data/pelvic.score.rda
paleoTS/data/pterygiophores.rda
paleoTS/R
paleoTS/R/paleoTS_0.5-1.R
paleoTS/MD5
paleoTS/DESCRIPTION
paleoTS/man
paleoTS/man/fit3models.Rd
paleoTS/man/fitGpunc.Rd
paleoTS/man/as.paleoTSfit.Rd
paleoTS/man/sim.punc.Rd
paleoTS/man/test.var.het.Rd
paleoTS/man/ESD.Rd
paleoTS/man/cat.paleoTS.Rd
paleoTS/man/mle.GRW.Rd
paleoTS/man/sim.GRW.Rd
paleoTS/man/compareModels.Rd
paleoTS/man/as.paleoTS.Rd
paleoTS/man/opt.covTrack.Rd
paleoTS/man/logL.joint.GRW.Rd
paleoTS/man/fit.sgs.Rd
paleoTS/man/fitSimple.Rd
paleoTS/man/fitModeShift.Rd
paleoTS/man/LRI.Rd
paleoTS/man/ln.paleoTS.Rd
paleoTS/man/opt.joint.GRW.Rd
paleoTS/man/opt.GRW.Rd
paleoTS/man/stickleback.Rd
paleoTS/man/bootSimpleComplex.Rd
paleoTS/man/opt.GRW.shift.Rd
paleoTS/man/IC.Rd
paleoTS/man/sim.covTrack.Rd
paleoTS/man/plot.paleoTS.Rd
paleoTS/man/fitMult.Rd
paleoTS/man/modelCurves.Rd
paleoTS/man/sim.OU.Rd
paleoTS/man/lynchD.Rd
paleoTS/man/paleoTS-package.Rd
paleoTS/man/std.paleoTS.Rd
paleoTS/man/sub.paleoTS.Rd
paleoTS/man/logL.GRW.Rd