Analyze Paleontological Time-Series

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Documentation for package ‘paleoTS’ version 0.6.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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