LBSPRopt: Optimisation Routine for fitting LBSPR

In AdrianHordyk/LBSPR: Length-Based Spawning Potential Ratio

Optimisation Routine for fitting LBSPR

Description

A function that calculate the negative log-likelihood of the LBSPR model

Usage

LBSPRopt(
  trypars,
  yr = 1,
  LB_pars = NULL,
  LB_lengths = NULL,
  Control = list(),
  pen = TRUE
)

Arguments

trypars	a vector of exploitation parameters in log space
yr	index of the year column to fit the model to
LB_pars	an object of class 'LB_pars' that contains the life history information
LB_lengths	an object of class 'LB_lengths' that contains the length data
Control	a list of control options for the LBSPR model.
pen	apply a penalty if estimate of selectivity is very high?

Details

The Control options are:

modtype

Model Type: either Growth-Type-Group Model (default: "GTG") or Age-Structured ("absel")

maxsd

Maximum number of standard deviations for length-at-age distribution (default is 2)

ngtg

Number of groups for the GTG model. Default is 13

P

Proportion of survival of initial cohort for maximum age for Age-Structured model. Default is 0.01

Nage

Number of pseudo-age classes in the Age Structured model. Default is 101

maxFM

Maximum value for F/M. Estimated values higher than this are trunctated to maxFM. Default is 4

Value

a NLL value

Author(s)

A. Hordyk

AdrianHordyk/LBSPR documentation built on July 21, 2023, 6:27 p.m.