make.fit: make.fit: fit APAM

In SineAndie/APAM: APAM: American plaice assessment model

Description

Fits American plaice assessment model (APAM).

Usage

make.fit(
  data,
  map,
  parameters,
  do.sd = TRUE,
  do.Zresid = TRUE,
  do.NS = TRUE,
  do.hess = FALSE,
  NS = 4
)

Arguments

data	object returned from make.tmb.data
map	object returned from make.map
parameters	object returned from make.parm
do.sd	(optional) T/F, run sdreport? Default = TRUE.
do.Zresid	(optional) T/F, get adjusted residuals? Default = TRUE.
do.NS	(optional) T/F, do extra Newton steps? Default = TRUE.
do.hess	(optional) calculate hessian? Default = TRUE.
NS	(optional) positive integer, set numer of Newton setps. Default = 4.

Value

returns a list containing:

$obj

object from TMB::MakeADFun

$opt

results from stats::nlminb

$rep

report from obj$report() from MakeADFun

$sdrep

if do.sd=T returns sdreport from MakeADFun

$sdrep1

if do.Zresid=T returns sdreport from residuals from MakeADFun

$tmb.data

object from make.tmb.data that was used in the model

$map

object from make.map that was used in the model

$parameters

object from make.parm that was used in the model

$hess

if do.hess=T returns hessian

Examples

## Not run: 
fit <- make.fit(data, map, parameters)

## End(Not run)

SineAndie/APAM documentation built on Dec. 18, 2021, 2:05 p.m.