make.profile: make.profile: calculate profile likelihoods

In SineAndie/APAM: APAM: American plaice assessment model

Description

Calculates profile likelihoods for APAM for individual data components.

Usage

make.profile(mfits, delta_M = NULL)

Arguments

mfits	object returned from make.fit
delta_M	(optional) vector, to manually set range of M perturbations. Default delta_M <- seq(-0.15,0.40, by = 0.01).

Value

Returns marginal profile for age composition data and remainder/conditional for surveys and landings data. Additionally, components from the joint negative log-likelihood are also returned.

$conditional

conditional profile likelihoods for surveys and landings data

$remainder

remainder profile likelihoods for surveys and landings data

$marginal

marginal profile likelihoods for age composition data

$conditional_dev

conditional profile likelihood deviations for surveys and landings data

$remainder_dev

remainder profile likelihood deviations for surveys and landings data

$marginal_dev

marginal profile likelihood deviationsfor age composition data

$joint

joint profile likelihoods for all data components

$joint_dev

joint profile likelihood deviations for all data components

$conv_fit

returns max inner and outer gradients for M perturbed model fit and convergence message from optimization

$no.gr2

returns perturbation number and error message if error is returned during netwon steps

Examples

## Not run: 
profile <- make.profile(mfits)

## End(Not run)

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