R: Analyze Paleontological Time-Series

# Analyze Paleontological Time-Series

## Documentation for package ‘paleoTS’ version 0.6.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

akaike.wts | Compute Akaike weights from AIC scores
as.paleoTS | Make a Paleontological Time-series object
as.paleoTSfit | Create a 'paleoTSfit' object
bootSimpleComplex | Bootstrap test to see if a complex model is significantly better than a simple model.
cantius_L | Time-series of the length of lower first molar for the Cantius lineage
checkSSMresiduals | Compute and (optionally) plot residuals from SSM model fit
compareModels | Compare model fits for a paleontological time-series
dorsal.spines | Time-series of dorsal spine data from a fossil stickleback lineage
ESD | Compute Expected Squared Divergence (ESD) for Evolutionary Models
fit.sgs | Fit a model of trait evolution with a protracted punctuation.
fit3models | Fit a set of standard evolutionary models
fit4models | Fit a set of standard evolutionary models
fit9models | Fit large set of models to a time-series
fitGpunc | Fit trait evolution model with punctuations estimated from the data
fitModeShift | Fit model in which the mode of trait evolution shifts once
fitMult | Fit the same simple model across multiple time-series
fitSimple | Fit simple models of trait evolution
IC | Compute Information Criteria
Kfiltertv | Time-varying Kalman filter calculations
ln.paleoTS | Approximate log-transformation of time-series data
LRI | Log-rate, Log-interval (LRI) method of Gingerich
lynchD | Compute Lynch's Delta rate metric
mle.GRW | Analytical ML estimator for random walk and stasis models
mle.Stasis | Analytical ML estimator for random walk and stasis models
mle.URW | Analytical ML estimator for random walk and stasis models
opt.covTrack | Fit a model in which a trait tracks a covariate
opt.GRW | Fit evolutionary model using "AD" parameterization
opt.GRW.shift | Fit random walk model with shift(s) in generating parameters
opt.joint.covTrack | Fit a model in which a trait tracks a covariate
opt.joint.GRW | Fit evolutionary models using the "Joint" parameterization
opt.joint.OU | Fit Ornstein-Uhlenbeck model using the "Joint" parameterization
opt.joint.punc | Fit a model of trait evolution with specified punctuation(s)
opt.joint.Stasis | Fit evolutionary models using the "Joint" parameterization
opt.joint.StrictStasis | Fit evolutionary models using the "Joint" parameterization
opt.joint.URW | Fit evolutionary models using the "Joint" parameterization
opt.punc | Fit a model of trait evolution with specified punctuation(s)
opt.ssm.ACDC | Fit evolutionary models using state-space models (SSM)
opt.ssm.covOU | Fit evolutionary models using state-space models (SSM)
opt.ssm.covOU_vshift | Fit evolutionary models using state-space models (SSM)
opt.ssm.GRW | Fit evolutionary models using state-space models (SSM)
opt.ssm.OU | Fit evolutionary models using state-space models (SSM)
opt.ssm.Stasis | Fit evolutionary models using state-space models (SSM)
opt.ssm.StrictStasis | Fit evolutionary models using state-space models (SSM)
opt.ssm.URW | Fit evolutionary models using state-space models (SSM)
opt.ssm.URWshift | Fit evolutionary models using state-space models (SSM)
opt.Stasis | Fit evolutionary model using "AD" parameterization
opt.StrictStasis | Fit evolutionary model using "AD" parameterization
opt.URW | Fit evolutionary model using "AD" parameterization
plot.paleoTS | Plot a paleoTS object
pool.var | Compute a pooled variance
print.paleoTSfit | Print a paleoTSfit object
read.paleoTS | Read a text-file with data from a paleontological time-series
sim.covTrack | Simulate trait evolution that tracks a covariate
sim.GRW | Simulate random walk or directional time-series for trait evolution
sim.GRW.shift | Simulate (general) random walk with shift(s) in generating parameters
sim.OU | Simulate an Ornstein-Uhlenbeck time-series
sim.punc | Simulate a punctuated time-series
sim.sgs | Simulate protracted punctuation
sim.Stasis | Simulate Stasis time-series for trait evolution
sim.Stasis.RW | Simulate trait evolution with a mode shift
std.paleoTS | Convert time-series to standard deviation units
sub.paleoTS | Subsample a paleontological time-series
test.var.het | Test for heterogeneity of variances among samples in a time-series