opt.joint.OU: Fit Ornstein-Uhlenbeck model using the "Joint"...

In paleoTS: Analyze Paleontological Time-Series

Fit Ornstein-Uhlenbeck model using the "Joint" parameterization

Description

Fit Ornstein-Uhlenbeck model using the "Joint" parameterization

Usage

opt.joint.OU(
  y,
  pool = TRUE,
  cl = list(fnscale = -1),
  meth = "L-BFGS-B",
  hess = FALSE
)

Arguments

y	a paleoTS object
pool	if TRUE, sample variances are substituted with their pooled estimate
cl	optional control list, passed to optim()
meth	optimization algorithm, passed to optim()
hess	if TRUE, return standard errors of parameter estimates from the hessian matrix

Details

This function fits an Ornstein-Uhlenbeck (OU) model to time-series data. The OU model has four generating parameters: an ancestral trait value (anc), an optimum value (theta), the strength of attraction to the optimum (alpha), and a parameter that reflects the tendency of traits to diffuse (vstep). In a microevolutionary context, these parameters can be related to natural selection and genetic drift; see Hunt et al. (2008).

Value

a paleoTSfit object with the model fitting results

Note

It is easier to use the convenience function fitSimple. Note also that preliminary work found that the "AD" parameterization did not perform as well for the OU model and thus it is not implemented here.

References

Hunt, G., M. A. Bell and M. P. Travis. 2008. Evolution toward a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage. Evolution 62(3): 700-710.

See Also

fitSimple, opt.joint.GRW

Examples

x <- sim.OU(vs = 0.5)  # most defaults OK
w <- opt.joint.OU(x)
plot(x, modelFit = w)

paleoTS documentation built on Aug. 9, 2022, 1:06 a.m.