change_e: Methods to alter which parameters are estimated in a SS3...
In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description Usage Arguments Details Value Which arguments to specifiy in case files Author(s) See Also Examples

Takes SS3 .ctl and forecast.ss files, along with a list structure which houses the data file as read in by SS_readdat and changes which parameters are estimated, how natural mortality is estimated, and if forecasts are performed. The function can be called by itself or within run_ss3sim to alter an estimation model .ctl file. If used with run_ss3sim the case file should be named E. A suggested (default) case letter is E for estimation.

change_e(ctl_file_in = "em.ctl", ctl_file_out = "em.ctl",
  dat_list = NULL, for_file_in = "forecasts.ss", par_name = NULL,
  par_int = "NA", par_phase = "NA", forecast_num = 0,
  verbose = FALSE, natM_type = NULL, natM_n_breakpoints = NULL,
  natM_lorenzen = NULL, natM_val = NULL)

`ctl_file_in`	A string providing the path to the input SS `.ctl` file.
`ctl_file_out`	A string providing the path to the output SS control file. If the value is `NULL`, the file will not be written to the disk.
`dat_list`	An SS data list object as read in from `SS_readdat` in the r4ss package. Make sure you select option `section=2`.
`for_file_in`	A string providing the path to the input SS `forecast.ss` file.
`par_name`	*A vector of values, separated by commas. Each value corresponds to a parameter that you wish to turn on or off in the `ctl_file_in`. The values will later be turned into character values and used to search for specific lines for each parameter in the `ctl_file_in`, therefore it is best to use full parameter names as they are specified in `ctl_file_in`.
`par_int`	*A vector of initial values, one for each parameter in `par_name`. Values can be `NA` if you do not wish to change the initial value for a given parameter.
`par_phase`	*A vector of phase values, one for each parameter in `par_name`. Values can be `NA` if you do not wish to change the phase for a given parameter.
`forecast_num`	*Number of years to perform forecasts. For those years, the data will be removed from the `dat_list`, enabling SS3 to generate forecasts rather than use the data to fit the model.
`verbose`	When `TRUE` messages will be returned from the function. Often useful for debugging. The default is `FALSE`.
`natM_type`	Deprecated. Should have value NULL.
`natM_n_breakpoints`	Deprecated. Should have value NULL.
`natM_lorenzen`	Deprecated. Should have value NULL.
`natM_val`	Deprecated. Should have value NULL.

Turning parameters on and off is the main function of change_e. change_e was not created with the capability of adding parameters to a .ctl file. The function can only add parameters for age specific natural mortality, and only for models with one growth morph. Furthermore, the function is designed to add complexity to the natural mortality type and not remove complexity. Therefore, the function will fail if natural mortality in the ctl_file_in is not specified as "1Param" and natM_type is anything other than NULL or "1Param".

Altered versions of SS3 .ctl and forecast.ss files are written to the disk and the altered dat_list is returned invisibly.

All function argument descriptions that start with an asterisk (*) will be passed through the case files to run_ss3sim. If one of these arguments is not specified in a case file, then a value of NULL will be passed, which may or may not be an appropriate value. Other arguments will be ignored if specified.

Kelli Johnson

Other change functions: change_data, change_em_binning, change_f_par, change_f, change_o, change_retro, change_tv

## Not run: 

d <- system.file("extdata", "models", "cod-om", package = "ss3sim")
data.old <- r4ss::SS_readdat(
  system.file("extdata", "models", "cod-om", "codOM.dat",
    package = "ss3sim"),
  version = NULL, verbose = FALSE)
change_e(
  ctl_file_in = file.path(d, "codOM.ctl"),
  ctl_file_out = file.path(tempdir(), "change_e.ctl"),
  dat_list = data.old,
  for_file_in = file.path(d, "forecast.ss"),
         natM_type = NULL, natM_n_breakpoints = NULL,
         natM_lorenzen = NULL, natM_val = NULL,
         par_name = c("_steep", "SizeSel_P1_Fishery(1)"),
         par_int = c(0.3, 40), par_phase = c(3, 2),
         forecast_num = 0)
# clean up the temporary files
file.remove(file.path(tempdir(), "change_e.ctl"))

## End(Not run)