Update use of superseded functions

[ddsjoberg]

There are three superseded functions currently being used in the variable listings. And we need to make updates to no longer use them.

we need to identify a few things:

• these variables come from a template in the respective package. does the template need to be updated? if so, that will need to happen before we update.
• if the template has already been updated to use a non-superseded function, then we can simply update our CSV file.

@athenamelia is this something you have the bandwidth to work on?

[bms63]

Sorry to hijack your issue!! Can we get this test to run run on the templates and vignettes in admiral??!!

[ddsjoberg]

Kind of? maybe? idk?

We'd need to ingest the entire template script, parse it in such a way where we extract every function used, then take that list of functions and compare it the the list of superseded/deprecated functions (which we can get that list using functions in admiraldiscovery).

So that first bit it going to be tricky I think, unless someone has a script/function to do this....

ok, after two seconds of searching:
here's a method using a script someone wrote on the posit community forum: https://community.rstudio.com/t/is-there-a-way-to-extract-the-names-of-all-functions-in-an-r-script/51905
here's a function in a package that looks like it'll do it as well: https://rdrr.io/cran/NCmisc/man/list.functions.in.file.html

[ddsjoberg]

how/where do you want this to work? i don't think it belongs in the individual packages. maybe this could be more warnings here in admiraldiscovery?

[bms63]

I was thinking it would be a test in admiral where we could grab the @superseded functions and make sure none of them are being used in the templates.

I wonder if something from logrx could be used?
https://github.com/pharmaverse/logrx/blob/4e078732bebc031c0bd00120fe336fb1a91ff76e/R/get.R#L137

but the list.functions.in.file looks really easy...maybe we could just borrow the code rather than put NCmisc in the suggests

> list.functions.in.file function (filename, alphabetic = TRUE) { if (!file.exists(filename)) { stop("couldn't find file ", filename) } if (!get.ext(filename) == "R") { warning("expecting *.R file, will try to proceed") } tmp <- getParseData(parse(filename, keep.source = TRUE)) nms <- tmp$text[which(tmp$token == "SYMBOL_FUNCTION_CALL")] funs <- unique(if (alphabetic) { sort(nms) } else { nms }) src <- paste(as.vector(sapply(funs, find))) outlist <- tapply(funs, factor(src), c) return(outlist) }

[bms63]

I guess at the end of the day - I just want something that alerts me to superseded functions or deprecated functions being used. It can live where ever, but I just want it to be something that is continuously checked.

[ddsjoberg]

Hmmm, let's think about the best ways to make this work and discuss at our meeting? I agree we shouldn't add dependencies to make this work.