run_sensitivities: Run sensitivities for a base model

In iantaylor-NOAA/Lingcod_2021: Estimate the Status of Lingcod off the US West Coast in 2021

Run sensitivities for a base model

Description

Run sensitivities for a base model

Usage

run_sensitivities(
  dirbase,
  type = c("profile", "retro", "regularization", ),
  numbers = 1:999,
  extras = "-nox -nohess -cbs 1500000000",
  skipfinished = TRUE
)

Arguments

dirbase	The directory that has the base-model files. This path needs to be full or relative to your current location.
type	The type of sensitivity you want to run. Options are "profile", "retro", "regularization", "sens_create", and "sens_run".
numbers	Numbers of specific sensitivities to create or run.
extras	additional arguments after the "ss" command passed to 'r4ss::run_SS_
skipfinished	skip directories with existing Report.sso files (passed to r4ss::SS_changepars()). Doesn't apply to profiles, retros, or regularization.
dir	the source model directory
num	the senstiviity number as represented in sensitivity.csv
suffix	a string to append to the new path wrapper for r4ss::copy_SS_inputs() with defaults for run_sensitivies() convert values from the CSV file into format required by r4ss::SS_changepars(), including splitting multiple entries

Author(s)

Kelli Faye Johnson, Ian G. Taylor

Examples

## Not run: 
dirbase <- get_dir_ling(area = area, num = 14, sens = 1)
run_sensitivities(dirbase, c("profile", "retro", "regularization"))
run_sensitivities(get_dir_ling("n", 22),
                  type = "sens_create",
                  numbers = c(102, 104))
run_sensitivities(get_dir_ling("s", 14),
                  type = c("sens_run", "sens_create"),
                  numbers = c(303:320))

## End(Not run)
create a path associated with a particular sensitivity
by converting a source directory, like
"2021.n.016.001_tune" to a sensitivity path like
"2021.n.016.101_shareM".

iantaylor-NOAA/Lingcod_2021 documentation built on Oct. 30, 2024, 6:42 p.m.