MSEtool (version 3.1.1)

iSCAM2OM: Reads MLE estimates from iSCAM file structure into an operating model

Description

A function that uses the file location of a fitted iSCAM model including input files to population the various slots of an operating model parameter estimates. iSCAM2OM relies on several functions written by Chris Grandin (DFO PBS).

Usage

iSCAM2OM(
  iSCAMdir,
  nsim = 48,
  proyears = 50,
  mcmc = F,
  Name = NULL,
  Source = "No source provided",
  length_timestep = 1,
  nyr_par_mu = 2,
  Author = "No author provided",
  report = F,
  silent = F
)

Arguments

iSCAMdir

A folder with iSCAM input and output files in it

nsim

The number of simulations to take for parameters with uncertainty (for OM@cpars custom parameters)

proyears

The number of MSE projection years

mcmc

Whether to use mcmc samples to create custom parameters cpars

Name

The name of the operating model

Source

Reference to assessment documentation e.g. a url

length_timestep

How long is a model time step in years (e.g. a quarterly model is 0.25, a monthly model 1/12)

nyr_par_mu

integer, the number of recent years to estimate vulnerability over for future projections

Author

Who did the assessment

report

logical should a numbers at age reconstruction plot be produced?

silent

logical should progress reporting be printed to the console?