change_rec_devs: Replace recruitment deviations
In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description Usage Arguments Details Value Author(s) Examples

This function replaces the recruitment deviations in the control file of a Stock Synthesis model with those specified in the argument recdevs. The new control file is then written to the disk if ctl_file_out is specified. It is imperative that the path provided in ctl_file_in be to a ss_new file so change_rec_devs can properly determine where to place the recruitment deviations in the control file.

1 2	change_rec_devs(recdevs, ctl_file_in, ctl_file_out = "control_recruitment.ss")

`recdevs`	A vector of recruitment deviations to be entered into the SS control file. The vector must be the same length as the vector of recruitment deviations that are commented out in the `ss_new` control file. This vector can be found by searching for `# all recruitment deviations` within the file. If a single value is provided instead of a vector, the value will be repeated for every recruitment deviation in the model. Alternatively, users can supply a named vector with each name being a year of the model. Missing years will be filled in with values of zero.
`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.

This function does not need to be specified in a case file if you are running an ss3sim simulation using run_ss3sim.

A modified SS control file.

Kelli Faye Johnson

d <- system.file(file.path("extdata", "models"), package = "ss3sim")
change_rec_devs(recdevs = rlnorm(101),
  ctl_file_in = file.path(d, "cod-om", "codOM.ctl"),
  ctl_file_out = file.path(tempdir(), "control_recdevs.ss"))
# Change the recruitment deviations in years 2:11
change_rec_devs(recdevs = setNames(rlnorm(10), 2:11),
  ctl_file_in = file.path(d, "cod-om", "codOM.ctl"),
  ctl_file_out = file.path(tempdir(), "control_recdevsInitial.ss"))
sapply(dir(tempdir(), pattern = "control_.+ss", full.names = TRUE), unlink)