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Modify variance and sample size adjustments in the control file

Source: R/SS_varadjust.R
SS_varadjust.Rd

Function has not been fully tested yet

Usage

SS_varadjust(
  dir = "C:/myfiles/mymodels/myrun/",
  ctlfile = "control.ss_new",
  newctlfile = "control_modified.ss",
  keyword = "variance adjustments",
  newtable = NULL,
  newrow = NULL,
  rownumber = NULL,
  maxcols = 100,
  maxrows = 100,
  overwrite = FALSE,
  version = "3.30",
  verbose = TRUE
)

Arguments

dir

A file path to the directory of interest. The default value is dir = NULL, which leads to using the current working directory.

ctlfile

Control file name. Default="control.ss_new".

newctlfile

Name of new control file to be written. Default="control_modified.ss".

keyword

Keyword to use as reference for start of section on variance adjustments

newtable

Optional table of new variance adjustment values

newrow

Optional vector of new variance adjustment values for a particular row

rownumber

Which of the 6 rows to replace with 'newrow' if present?

maxcols

Maximum number of columns to search among in 3.24 models (may need to increase from default if you have a huge number of fleets)

maxrows

Maximum number of rows to search among in 3.30 models (may need to increase from default if you have a huge number of fleets)

overwrite

A logical value specifying if the existing file(s) should be overwritten. The default value is overwrite = FALSE.

version

SS version number. Currently "3.24" or "3.30" are supported, either as character or numeric values (noting that numeric 3.30 = 3.3). version = NULL is no longer the default or an allowed entry. The default is version = "3.30".

verbose

A logical value specifying if output should be printed to the screen.

See also

tune_comps(), SS_parlines(), SS_changepars()

Author

Ian G. Taylor, Gwladys I. Lambert

Examples

if (FALSE) {
# load model output into R
replist <- SS_output(dir = "c:/model/")

# get new variance adjustments (
varadjust <- tune_comps(replist, option = "Francis")
print(varadjust)

# write new table to file
SS_varadjust(
  dir = replist[["inputs"]][["dir"]], newctlfile = "new_control.ss",
  newtable = varadjust, overwrite = FALSE
)
}