Verify and standardize Stock Synthesis input files

Source: R/verify_input.r

Verify the contents of operating model (OM) and estimation model (EM) folders, i.e., check that the necessary Stock Synthesis input files are available. If the contents are correct, the .ctl and .dat files are renamed to standardized names and the starter.ss file is updated to reflect these names. If the contents are incorrect, then a warning is issued and the simulation is aborted.

verify_input(model_dir, type = c("om", "em"))

Arguments

model_dir

Directory name for model. This folder should contain the .ctl, .dat, files etc.

type

One of "om" or "em" for operating or estimating model.

Value

Nothing is returned from this function. Instead, file are changed and saved to the disk.

Author

Curry James Cunningham; modified by Sean Anderson

Examples

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

d <- system.file("extdata", "models", package = "ss3sim")

om <- file.path(d, "cod-om")
em <- file.path(d, "cod-em")

file.copy(om, temp_path, recursive = TRUE)
#> [1] TRUE
file.copy(em, temp_path, recursive = TRUE)
#> [1] TRUE

# Verify the correct files exist and change file names:
verify_input(model_dir = file.path(temp_path, "cod-om"), type = "om")
verify_input(model_dir = file.path(temp_path, "cod-em"), type = "em")
unlink(temp_path, recursive = TRUE)