change_retro function

Alter a starter file for a retrospective analysis

A retrospective analysis tests the effect of peeling back the number of operating model years observable to the estimation model. This function alters the SS3 starter file to run a retrospective analysis. If used with run_ss3sim the case file should be named R. A suggested (default) case letter is R.

change_retro(str_file_in = "starter.ss", str_file_out = "starter.ss",
  retro_yr = 0)

Arguments

• str_file_in: A string providing the path to the input SS starter.ss file.
• str_file_out: A string providing the path to the output SS starter.ss file.
• retro_yr: *Which retrospective year to enter into the starter file. Should be 0 (no retrospective analysis) or a negative value.

Returns

A modified SS3 starter file.

Details

Note that the starter file is set up to run a single retrospective run. Therefore, if you would like to run retrospective analyses for, say, 0, 1, 2, 3, 4, and 5 years, you will need to use this function to adjust the starter file 6 separate times.

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.

Examples

# Create a temporary folder for the output:
temp_path <- file.path(tempdir(), "ss3sim-retro-example")
dir.create(temp_path, showWarnings = FALSE)

# Locate the package data:
starterfile <- system.file("extdata", "models", "cod-om",
 "starter.ss", package = "ss3sim")

# No retrospective analysis:
change_retro(starterfile, paste0(temp_path, "/retro-0-starter.ss"),
retro_yr = 0)

# A retrospective analysis of 5 years:
change_retro(starterfile, paste0(temp_path, "/retro-5-starter.ss"),
retro_yr = -5)

See Also

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

Author(s)

Sean C. Anderson