maxLikPOUMMGivenTreeVTips {POUMM}

Find a maximum likelihood fit of the POUMM model

Description

Find a maximum likelihood fit of the POUMM model

Usage

maxLikPOUMMGivenTreeVTips(
  loglik,
  pruneInfo,
  parLower,
  parUpper,
  parInitML = NULL,
  control = list(factr = 1e+08, fnscale = -1),
  verbose = FALSE,
  debug = FALSE,
  ...
)

Arguments

loglik

function(par, memo, parFixedNoAlpha)

pruneInfo

a list-object returned by the pruneTree(tree, z) function.

parLower, parUpper

Two named numeric vectors indicating the boundaries of the search region. Default values are parLower = c(alpha = 0, theta = 0, sigma = 0, sigmae = 0) and parUpper = c(alpha = 100, theta = 10, sigma = 20, sigmae = 10).

parInitML

A named vector (like parLower and parUpper) or a list of such vectors - starting points for optim.

control

List of parameters passed on to optim, default list(factr = 1e8, fnscale = -1), see ?optim.

verbose

A logical indicating whether to print informative messages on the standard output.

debug

A logical indicating whether to print debug messages (currently not implemented).

...

currently not used.

Value

a list containing an element par and an element value as well as the parameters passed