get_caseargs: Take a scenario ID and return argument lists

Description Usage Arguments Details Value Examples

View source: R/case-parsing.r


This function calls a number of internal functions to go from a unique scenario identifier like "D1-E2-F3-M0-R4-cod" and read the corresponding input files (e.g. "M0-cod.txt") that have two columns: the first column contains the argument names and the second column contains the argument values. The two columns should be separated by a semicolon. The output is then returned in a named list with the intention of passing these to run_ss3sim or ss3sim_base.


get_caseargs(folder, scenario, ext = ".txt", case_files = list(F = "F",
  D = c("index", "lcomp", "agecomp")))



The folder to look for input files in.


A character object that has the cases separated by the "-" delimiter. The combination of cases and stock ID is referred to as a scenario. E.g. "D0-E0-F0-M0-R0-cod". See the Details section.


The file extension of the input files. Defaults to ".txt".


A named list that relates the case IDs (e.g. "D") to the files to read the arguments from (e.g. c("index", "lcomp", "agecomp")). See the Details section.


Let's start with an example scenario "D0-E1-F0-M0-R0-cod". The single capital letters refer to case IDs. The numbers refer to the case numbers. The last block of text (cod) represents the stock ID (any alphanumeric string of text will work) and is to help the user identify different "stocks" (intended to represent different SS3 model setups).

The stock IDs should correspond to how the case files are named and the case IDs should correspond to the cases described by the case_files. The case file names will correspond to the list values plus the stock ID. For example list(D = c("index", "lcomp", "agecomp")) combined with the stock ID cod means that the case D1 will refer to the case files index-cod.txt, lcomp-cod.txt, agecomp-cod.txt.

The case argument plain text files should have arguments in the first column that should be passed on to functions. The names should match exactly. The second column (delimited by a semicolon) should contain the values to be passed to those arguments. Multiple words should be enclosed in quotes.

You can use any simple R syntax to declare argument values. For example: c(1, 2, 4), or seq(1, 100), or 1:100, or matrix(), or NULL. Character objects don't need to be quoted, but can be if you'd like. However, be careful not to use the delimiter (set up as a semicolon) anywhere else in the file besides to denote columns. You can add comments after any # symbol just like in R.

Internally, the functions evaluate in R any entries that have no character values (e.g. 1:100), or have an alpha-numeric character followed by a (. Anything that is character only or has character mixed with numeric but doesn't have the regular expression "[A-Za-z0-9](" gets turned into a character argument. (NA and NULL are special cases that are also passed on directly.)


A (nested) named list. The first level of the named list refers to the case_files. The second level of the named list refers to the argument names (the first column in the input text files). The contents of the list are the argument values themselves (the second column of the input text files).


# Find the example data folders:
case_folder <- system.file("extdata", "eg-cases", package =

# An example using the cases defined by default:
get_caseargs(case_folder, scenario = "D0-F0-cod")

# With a custom time-varying case for selectivity, which we'll call
# the S case. Here, we'll need to define which file the case S should
# read from ("S*-cod.txt"):
get_caseargs(case_folder, scenario = "D0-E0-F0-M0-R0-S0-cod",
  case_files = list(E = "E", D = c("index", "lcomp", "agecomp"), F =
    "F", M = "M", R = "retro", S = "S"))

ss3sim documentation built on Nov. 9, 2019, 1:06 a.m.