R: Methods to include parameters in an SS3operating model

change_o {ss3sim}

R Documentation

Methods to include parameters in an SS3operating model

Description

change_o takes an SS3 .ctlfile and implements parameter value changes that are NOT time varying. change_o is specifically set up to work with an operating model .ctl file.

Usage

change_o(change_o_list, ctl_file_in = "control.ss_new",
  ctl_file_out = "om.ctl", par_name = NULL, par_int = NULL,
  verbose = FALSE)

Arguments

`change_o_list`	*A list of named vectors. Names correspond to parameters in the operating model and the vectors correspond to deviations. Alternatively, `par_name` and `par_init` can be passed to this function.
`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.
`par_name`	*A character vector of parameter names to pass in. NULL unless want to use instead of `change_o_list`.
`par_int`	*A numeric vector of parameter initial values to pass in. NULL unless want to use instead of `change_o_list`. Must have the same length and be in the same order as `par_names`, as the names should correspond with their initial values.
`verbose`	When `TRUE` messages will be returned from the function. Often useful for debugging. The default is `FALSE`.

Value

The function creates modified versions of the .ctl files. The function also returns change_o_list invisibly.

Which arguments to specifiy in case files

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.

Specifying the `change_o_list`

Parameters initial values will change according to the values passed to change_o_list. Each parameter should have a single value specified.

Parameter names must be unique and match the full parameter name in the .ctl file.

Passing arguments to `change_o` through `run_ss3sim`

(1) create a case file with an arbitrary letter not used elsewhere (anything but D, E, F, or R) and (2) include the line function_type; change_o in your case file. For example, you might want to use M for natural mortality, S for selectivity, or G for growth.

Author(s)

Kathryn Doering