R: Parsing boolean command line argument in using argparse - r

Question

I am using "argparse" library in R for command line arguments.
# Create parser
parser = ArgumentParser(description='command line args')
# Add command line arguments
parser$add_argument("is_local", nargs='?', type="logical",
help="whether to use local or server path", default=FALSE)
parser$add_argument("alert", nargs='?', type="double",
help="alert threshold", default=0.99)
I am trying to call it on command line such as:
Rscript my_func.R TRUE 0.99
However boolean argument does not change. Any idea how to parse boolean argument in R?
Thanks!

Answer 1

I don't know R, but the description of this package says it's a wrapper for the Python argparse.
I would recommend changing these:
parser$add_argument("is_local", nargs='?', type="logical",
help="whether to use local or server path", default=FALSE)
parser$add_argument("alert", nargs='?', type="double",
help="alert threshold", default=0.99)
to
parser$add_argument("--local", action='store_true'),
help="whether to use local or server path")
parser$add_argument("--alert", type="double",
help="alert threshold", default=0.99)
which would be called with
Rscript my_func.R --local --alert 0.99
store_true is illustrated on the basic docs page, https://github.com/trevorld/r-argparse
If I read the R correctly, your is_local should be giving you a warning
"You almost certainly want to use action='store_true' or action='store_false' instead"
A store_true argument sets the attribute to TRUE if present, and the default FALSE if absent. It should be an optional (--) and not set the nargs.
(It is possible to have an argument that takes strings 'true' and 'false' (or any other pair in your native language) and converts them to logical values, but requires more coding.)
I made --alert a flagged argument as well, without the nargs. Its value will be the default if absent, and the convert the string to a double if provided. It could be a '?' positional, but while learning I think it's best to stick with optionals unless you want the argument to be required.
The R-argparse docs aren't very complete. You may need to refer to the Python docs, and experiment to get the translation right.
https://docs.python.org/3/library/argparse.html

Answer 2

Thanks for your time and help!
I would like to share my workaround for the problem as I find original argparse (action) usage a bit complicated.
# Convert str input to boolean
str2bool = function(input_str)
{
if(input_str == "0")
{
input_str = FALSE
}
else if(input_str == "1")
{
input_str = TRUE
}
return(input_str)
}
# Create parser
parser = ArgumentParser(description='command line args')
# Add command line arguments
parser$add_argument("is_local", nargs='?', type="character",
help="whether to use local or server path", default="1")
parser$add_argument("alert", nargs='?', type="double",
help="alert threshold", default=0.99)
# Parse arguments
args = parser$parse_args()
# Convert str arguments
args$is_local = str2bool(args$is_local)
# Call on CMD line
Rscript my_func.R 1 0.99 #equivalent Rscript my_func.R TRUE 0.99
Rscript my_func.R 0 0.99 #equivalent Rscript my_func.R FALSE 0.99

Answer 3

Below is the sample example given in the official docs of package argparse:
parser <- ArgumentParser(description='Process some integers')
parser$add_argument('integers', metavar='N', type="integer", nargs='+',
help='an integer for the accumulator')
parser$add_argument('--sum', dest='accumulate', action='store_const',
const='sum', default='max',
help='sum the integers (default: find the max)')
parser$print_help()
# default args for ArgumentParser()$parse_args are commandArgs(TRUE)
# which is what you'd want for an Rscript but not for interactive use
args <- parser$parse_args(c("--sum", "1", "2", "3"))
accumulate_fn <- get(args$accumulate)
print(accumulate_fn(args$integers))
Here is the link for the argparse pdf https://cran.r-project.org/web/packages/argparse/argparse.pdf
I hope it might help.