paleoTS-package |
Analysis of evoltuionary time-series |
add.OU.curves |
Adds curves to an existing plot indicating best-fit OU model |
akaike.wts |
Compute information criterion scores and Akaike weights for evoltuionary models |
as.paleoTS |
Paleontological time-series class |
cat.paleoTS |
Miscellaneous functions used internally for punctuations |
dorsal.spines |
Stickleback data from Bell et al. (2006) |
fit.sgs |
Analyze evolutionary models with well-sampled punctuations |
fit3models |
Do model fits for three standard evolutionary models |
fit3models.joint |
Do model fits for three standard evolutionary models |
fitGpunc |
Analyze evolutionary models with unsampled punctuations |
IC |
Compute information criterion scores and Akaike weights for evoltuionary models |
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 parameterization) |
logL.joint.OU |
Log-likelihoods for evolutionary models (joint parameterization) |
logL.joint.Stasis |
Log-likelihoods for evolutionary models (joint parameterization) |
logL.joint.URW |
Log-likelihoods for evolutionary models (joint parameterization) |
logL.Mult |
Functions to analyze multiple time-series jointly |
logL.punc |
Analyze evolutionary models with unsampled punctuations |
logL.punc.omega |
Analyze evolutionary models with unsampled punctuations |
logL.SameMs |
Functions to analyze multiple time-series jointly |
logL.SameVs |
Functions to analyze multiple time-series jointly |
logL.sgs |
Analyze evolutionary models with well-sampled punctuations |
logL.sgs.omega |
Analyze evolutionary models with well-sampled punctuations |
logL.Stasis |
Compute log-likelihoods for random walk and stasis models |
logL.URW |
Compute log-likelihoods for random walk and stasis models |
lynchD |
Compute rate metric from Lynch (1990) |
mle.GRW |
Maximum likelihood parameter estimators |
mle.Stasis |
Maximum likelihood parameter estimators |
mle.URW |
Maximum likelihood parameter estimators |
opt.GRW |
Numerically find maximum likelihood solutions to evolutionary models |
opt.GRW.shift |
Functions for random walks with shifting parameters |
opt.joint.GRW |
Optimize evolutionary models (joint parameterization) |
opt.joint.OU |
Optimize evolutionary models (joint parameterization) |
opt.joint.Stasis |
Optimize evolutionary models (joint parameterization) |
opt.joint.URW |
Optimize evolutionary models (joint parameterization) |
opt.punc |
Analyze evolutionary models with unsampled punctuations |
opt.RW.Mult |
Functions to analyze multiple time-series jointly |
opt.RW.SameMs |
Functions to analyze multiple time-series jointly |
opt.RW.SameVs |
Functions to analyze multiple time-series jointly |
opt.sgs |
Analyze evolutionary models with well-sampled punctuations |
opt.Stasis |
Numerically find maximum likelihood solutions to evolutionary models |
opt.URW |
Numerically find maximum likelihood solutions to evolutionary models |
ou.M |
Simulate evolutionary time-series |
ou.V |
Simulate evolutionary time-series |
paleoTS |
Analysis of evoltuionary time-series |
pelvic.score |
Stickleback data from Bell et al. (2006) |
plot.paleoTS |
Plots paleoTS objects |
pool.var |
Variance heterogeneity test |
pterygiophores |
Stickleback data from Bell et al. (2006) |
read.paleoTS |
Paleontological time-series class |
shift2gg |
Miscellaneous functions used internally for punctuations |
shifts |
Miscellaneous functions used internally for punctuations |
sim.GRW |
Simulate evolutionary time-series |
sim.GRW.shift |
Simulate evolutionary time-series with changing dynamics |
sim.OU |
Simulate evolutionary time-series |
sim.punc |
Simulate evolutionary time-series with changing dynamics |
sim.sgs |
Simulate evolutionary time-series with changing dynamics |
sim.Stasis |
Simulate evolutionary time-series |
split4punc |
Miscellaneous functions used internally for punctuations |
std.paleoTS |
Standardize paleontological time series data |
sub.paleoTS |
Subset an evolutionary time series |
test.var.het |
Variance heterogeneity test |