fitGpunc: Fit trait evolution model with punctuations estimated from...

In paleoTS: Analyze Paleontological Time-Series

Fit trait evolution model with punctuations estimated from the data

Description

Fit trait evolution model with punctuations estimated from the data

Usage

fitGpunc(
  y,
  ng = 2,
  minb = 7,
  pool = TRUE,
  oshare = TRUE,
  method = c("Joint", "AD"),
  silent = FALSE,
  hess = FALSE,
  parallel = FALSE,
  ...
)

Arguments

y	a paleoTS object
ng	number of groups (segments) in the sequence
minb	minimum number of populations within each segment
pool	if TRUE, sample variances are substituted with their pooled estimate
oshare	logical, if TRUE, variance assumed to be shared (equal) across segments
method	parameterization to use: Joint or AD; see Details
silent	logical, if TRUE, progress updates are suppressed
hess	if TRUE, standard errors computed from the Hessian matrix are returned
parallel	logical, if TRUE, the analysis is done in parallel
...	other arguments, passed to optimization functions

Details

This function tests all possible shift points for punctuations, subject to the constraint that the number of populations in each segment is always >= minb. The shiftpoint yielding the highest log-likelihood is returned as the solution, along with the log-likelihoods (all.logl) of all tested shift points (GG).

The function uses opt.punc (if method = "AD") or opt.joint.punc (if method = "Joint") to do the fitting.

Value

a paleoTSfit object with the results of the model-fitting.

Note

Calculations can be sped up by setting parallel = TRUE, which uses functions from the doParallel package to run the bootstrap replicates in parallel, using one fewer than the number of detected cores.

See Also

fit9models, sim.punc

Examples

x <- sim.punc(ns = c(15, 15), theta = c(0,3), omega = c(0.1, 0.1))
w.punc <- fitGpunc(x, oshare = TRUE)
plot(x, modelFit = w.punc)

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