Fits a TMB model in phases, like ADMB: parameters are switched on in stages
rather than all at once, which stabilizes a difficult optimization. The
optimizer (nlminb by default) runs once per phase; at each phase the map holds
fixed any parameter whose phase is greater than the current phase, so
parameters turn on progressively as the phase counter advances. phases is a
tagged list giving each named parameter its integer phase; parameters not
listed are estimated from the first phase onward.
Usage
TMBphase(
data,
parameters,
map,
random,
phases,
model_name,
silent,
use_gradient = TRUE,
control = list(eval.max = 1e+09, iter.max = 1e+09, trace = 0)
)Arguments
- data
A list to be passed to TMB
- parameters
A list of parameters of the model
- map
a list of map object from the model
- random
A character vector of names of parameters that are random effects
- phases
Tagged list assigning each named parameter its integer phase (as returned by
set_phases()).- model_name
A string describing the model name. Must be the name of your .cpp file
- silent
logical. Suppress TMB's output. No default; phased fits set it.
- use_gradient
logical. If TRUE, uses gradient in optimization (default = TRUE).
- control
A list of control parameters. For details see
?nlminb