case_tv {ss3sim} | R Documentation |
Write time varying casefiles to the disk
Description
Use R code to write arguments to the disk, which will later be used in a ss3sim simulation.
Usage
case_tv(species, parameter, perc_change, outfile, dir_out = "cases",
dir_models = system.file("models", package = "ss3models"),
nyears = 100, verbose = FALSE)
Arguments
species |
A vector of species, for which a unique case file will be generated. |
parameter |
A character value specifying the parameter to add deviates to. The argument must match the parameter name exactly. |
perc_change |
A vector of percents, which will be used to add deviates
to the parameter specified in |
outfile |
A character value specifying the case letter and number used to save the file. |
dir_out |
A character value specifying the directory to save the
|
dir_models |
The path where the models are stored, such that
|
nyears |
The length time-series included in the model. The length of
|
verbose |
Useful for debugging to print output to screen. Default is
|
Author(s)
Peter Kuriyama
Examples
temp_path <- file.path(tempdir(), "cod")
dir.create(temp_path, showWarnings = FALSE)
d <- system.file("extdata", package = "ss3sim")
om <- file.path(d, "models", "cod-om")
ig <- file.copy(om, temp_path, recursive = TRUE)
ig <- file.rename(file.path(temp_path, "cod-om"), file.path(temp_path, "om"))
filenames <- dir(file.path(temp_path, "om"), full.names = TRUE)
ig <- file.rename(filenames, gsub("codOM\\.|ss\\.", "ss3.", filenames))
verify_input(file.path(temp_path, "om"), type = "om")
ig <- file.rename(file.path(temp_path, "om", "om.ctl"),
file.path(temp_path, "om", "ss3.ctl"))
case_tv(species = "cod", parameter = "NatM_p_1_Fem_GP_1",
perc_change = rep(0.5, 100), outfile = "G1",
dir_out = temp_path, dir_models = gsub("/cod", "", temp_path),
nyears = 100, verbose = TRUE)
unlink(temp_path, recursive = TRUE)