parse_all_named_cli_args: Parse command-line arguments to global environment

In epi-sam/SamsElves: Helper functions for the data science at IHME

Parse command-line arguments to global environment

Description

Add an arbitrary number of CLI args to a parser (default trailing args only), then assign to a chosen environment (default 'globalenv()'). By default, automatically assign logical and integer data types when they are detected among CLI arguments, e.g. 'true' is assigned as 'TRUE' and 5 is assigned as '5L'.

Usage

parse_all_named_cli_args(
  required_args = NULL,
  trailingOnly = TRUE,
  assign_logical = TRUE,
  assign_integer = TRUE,
  assign_NA = TRUE,
  assign_NULL = TRUE,
  split_comma_str = TRUE,
  allow_rebinding = TRUE,
  assignment_env = globalenv()
)

Arguments

required_args	[list] (optional; default = NULL) Named list of required arguments to parse, with data types if desired. If you do not wish to check data types, supply 'NA'. e.g. 'list(arg1 = "character", arg2 = NA)'. **NOTE:** Parsed args are all "character" by default. If you wish the parser to assign integer or logical data types, set 'assign_integer' or 'assign_logical' to 'TRUE', and then you may check those types as well.
trailingOnly	[lgl] if TRUE, only the trailing arguments are used - passed to 'commandArgs()'
assign_logical	[lgl] if TRUE, assign true/false in parsed args to 'TRUE'/'FALSE'
assign_integer	[lgl] if TRUE, assign solely numeric args to integer e.g. 5 to '5L'
assign_NA	[lgl] if TRUE, assign 'NA' in parsed args to 'NA'
assign_NULL	[lgl] if TRUE, assign 'NULL' in parsed args to 'NULL'
split_comma_str	[lgl] if TRUE, split comma-separated strings into vectors
allow_rebinding	[lgl] if TRUE, allow re-binding of variables in the chosen environment (i.e. lockBinding was already used - unlock and re-lock all passed args, if relevant)
assignment_env	[env] which environment to assign CLI arguments to as named variables

Details

This does not take advantage of argument defaults or types. See https://github.com/trevorld/r-argparse for documentation.

Value

[named list] named list of CLI arguments

See Also

Other job_submission: submit_job()

Examples

## Not run: 
cli_args <- parse_all_named_cli_args(
   trailingOnly   = TRUE,
   assign_logical = TRUE,
   assign_integer = TRUE,
   assign_NA      = TRUE,
   assign_NULL    = TRUE,
   assignment_env = globalenv()
)

## End(Not run)

epi-sam/SamsElves documentation built on June 12, 2025, 7 a.m.