make_sim_adfun: Create ADFun from simulated data

In jkbest2/spatq: Use spatially varying catchability to standardize fishery-dependent data

Create ADFun from simulated data

Description

Read in a simulated data set and construct a TMB ADFun for model fitting.

Usage

make_sim_adfun(
  study,
  repl,
  opmod,
  estmod = NULL,
  sub_df = NULL,
  spec_estd = NULL,
  root_dir = ".",
  max_T = NULL,
  index_step,
  ...
)

Arguments

study	Simulation study
repl	Replicate number
opmod	Operating model
estmod	Estimation model
sub_df	Data frame indicating subsampling strategy; see subsample_catch
spec_estd	List of logicals indicating which parameters are to be estimated, as output specify_estimated
root_dir	Directory to load data from
max_T	Last year of data to include
index_step	Index grid step size
...	Additional options to pass to prepare_adfun

Value

A TMB ADFun suitable for optimization

Author(s)

John Best

jkbest2/spatq documentation built on Sept. 22, 2022, 3:22 a.m.