Does {logrx} work with Rscript?

[thomas-neitmann]

I've seen that you can make use of {logrx} when using Rscript like so Rscript -e "axecute('my_file.R')". However, what about the case where the R script itself takes command line arguments by making use of {optparse} or other packages? Let's say my script has a pop-filter argument and usually I would call it like Rscript my_script.R --pop-filter "SAFFL == 'Y'". With the current design is there any way to leverage {logrx} in this case?

[nicholas-masel]

It seems possible. I'm not familiar with {optparse} but I made a script, test.R, and just had it print commandArgs(trailing = TRUE).

So I ran this:

Rscript -e "logrx::axecute('test.R')" --pop-filter "SAFFL == 'Y'"

And it returned:

[1] "--pop-filter" "SAFFL == 'Y'"

[kodesiba]

@thomas-neitmann does the above example from @nicholas-masel work?

[thomas-neitmann]

I can confirm this works 🎉

# test.R
library(optparse)

parser <- OptionParser(add_help_option = FALSE) |>
  add_option("--pop-filter", "store", "character") |>
  add_option("--anl-filter", "store", "character")

args <- parse_args(parser, convert_hyphens_to_underscores = TRUE)

print(args)

Rscript -e "logrx::axecute('test.r')" --pop-filter SAF --anl-filter HGB

$pop_filter
[1] "SAF"

$anl_filter
[1] "HGB"

[thomas-neitmann]

Thanks a lot for the suggestion @nicholas-masel. I hadn't even imagined that you could call Rscript with the -e option and be able to pass command line arguments to the script.

[nicholas-masel]

@thomas-neitmann No problem! Glad that worked for you. I learned something new too. That's the first I've seen optparse. I'm sure it will come in handy one day.