verify_input: Verify and standardize SS3 input files
In ss3sim: Fisheries Stock Assessment Simulation Testing with Stock Synthesis

Description Usage Arguments Details Value Author(s) Examples

This function verifies the contents of operating model (om) and estimation model (em) folders (i.e., it checks that the necessary SS 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.

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

`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.

This is a helper function to be used within the larger wrapper simulation functions.

Returns a version of the folder with sanitized files or an error if some files are missing.

Curry James Cunningham; modified by Sean Anderson

# 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", package = "ss3sim")

om <- paste0(d, "/models/cod-om")
em <- paste0(d, "/models/cod-em")

file.copy(om, temp_path, recursive = TRUE)
file.copy(em, temp_path, recursive = TRUE)

# Verify the correct files exist and change file names:
verify_input(model_dir = paste0(temp_path, "/cod-om"), type = "om")
verify_input(model_dir = paste0(temp_path, "/cod-em"), type = "em")
unlink(temp_path, recursive = TRUE)