R: Analyses of Evolutionary Time-Series

# Analyses of Evolutionary Time-Series

## Documentation for package ‘evoTS’ version 1.0.3

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

as.evoTS.multi.BW.acceldecel.fit | Class for fit to evolutionary sequence (time-series) models
as.evoTS.multi.BW.fit | Class for fit to evolutionary sequence (time-series) models
as.evoTS.multi.OU.fit | Class for fit to evolutionary sequence (time-series) models
as.evoTS.multi.URW.fit | Class for fit to evolutionary sequence (time-series) models
as.evoTS.multi.URW.shift.fit | Class for fit to evolutionary sequence (time-series) models
as.evoTSfit.OUBM | Class for fit to evolutionary sequence (time-series) models
diameter_S.yellowstonensis | Evolutionary sequence (time-series) of phenotypic change in diameter in the lineage Stephanodiscus yellowstonensis
fit.all.univariate | Fit all univariate models to an evolutionary sequence (time-series).
fit.mode.shift | Fit two models to two separate segments to an evolutionary sequence (time-series).
fit.multivariate.OU | Fit predefined multivariate Ornstein-Uhlenbeck models to multivariate evolutionary sequence (time-series) data.
fit.multivariate.OU.user.defined | Fit user-defined multivariate Ornstein-Uhlenbeck models to multivariate evolutionary sequence (time-series) data.
fit.multivariate.URW | Fit multivariate Unbiased Random Walk models to multivariate evolutionary sequence (time-series) data.
fit.multivariate.URW.shift | Fit separate multivariate Unbiased Random Walk models to two different segments of a multivariate evolutionary sequence (time-series).
logL.joint.accel.decel.single.R | Log-likelihoods for evolutionary models
logL.joint.accel.decel.single.R.zero.corr | Log-likelihoods for evolutionary models
logL.joint.accel_decel | Log-likelihoods for evolutionary models
logL.joint.multi.OUOU | Log-likelihoods for evolutionary models
logL.joint.multi.OUOU.user | Log-likelihoods for evolutionary models
logL.joint.multi.R | Log-likelihoods for evolutionary models
logL.joint.OU.BM | Log-likelihoods for evolutionary models
logL.joint.single.R | Log-likelihoods for evolutionary models
logL.joint.single.R.zero.corr | Log-likelihoods for evolutionary models
logL.joint.Stasis.OU | Log-likelihoods for evolutionary models
logL.joint.URW.URW | Log-likelihoods for evolutionary models
loglik.surface.accel | Calculate the log-likelihood surface for a part of parameter space
loglik.surface.decel | Calculate the log-likelihood surface for a part of parameter space
loglik.surface.GRW | Calculate the log-likelihood surface for a part of parameter space
loglik.surface.OU | Calculate the log-likelihood surface for a part of parameter space
loglik.surface.OUBM | Calculate the log-likelihood surface for a part of parameter space
loglik.surface.stasis | Calculate the log-likelihood surface for a part of parameter space
loglik.surface.URW | Calculate the log-likelihood surface for a part of parameter space
make.multivar.evoTS | Makes a multivariate data set of
opt.accel.single.R | Fit multivariate Unbiased Random Walk with increasing (exponential accelerating) rate of change through time.
opt.accel.single.R.zero.corr | Fit multivariate Unbiased Random Walk model with uncorrelated trait changes and with increasing (exponential accelerating) rate of change through time.
opt.decel.single.R | Fit multivariate Unbiased Random Walk with decreasing (exponential decaying) rate of change through time.
opt.decel.single.R.zero.corr | Fit multivariate Unbiased Random Walk model with uncorrelated trait changes and with decreasing (exponential decaying) rate of change through time.
opt.joint.accel | Fit an Unbiased Random Walk with an accelerating rate of change through time.
opt.joint.decel | Fit an Unbiased Random Walk with an decelerating rate of change through time.
opt.joint.OUBM | Fit an Ornstein-Uhlenbeck model with an optimum that evolves according to a Unbiased Random Walk.
opt.joint.URW.Stasis | Optimization and log-likelihoods for pairs of models.
opt.single.R | Fit multivariate Unbiased Random Walk model.
opt.single.R.zero.corr | Fit multivariate Unbiased Random Walk model with uncorrelated trait changes.
plotevoTS | Plot a paleoTS object
plotevoTS.multivariate | Plots multivariate evolutionary sequence (time-series) data set
ribs_S.yellowstonensis | Evolutionary sequence (time-series) of phenotypic change in the number of ribs in the lineage Stephanodiscus yellowstonensis
sim.accel.decel | Simulate an Unbiased Random Walk with an accelerating or decelerating rate of change through time.
sim.multi.OU | Simulate multivariate Ornstein-Uhlenbeck evolutionary sequence data sets
sim.multi.URW | Simulate multivariate evolutionary sequence data that evolve according to an Unbiased Random Walk
sim.OUBM | Simulate an Ornstein-Uhlenbeck process with optimum changing according to an unbiased random walk