Add test case for `baseline_timepoints` in `derive_blfl` function

[ShiyuC]

This PR touches https://github.com/pharmaverse/sdtm.oak/issues/59, bullet point 3.

• Modify the test case to cover the usage of baseline_timepoints.
• Add different examples for the function

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Package	Line Rate	Health
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Summary	93% (952 / 1019)	✔

[ShiyuC]

@edgar-manukyan @ramiromagno May I request your review of this small MR? Thanks in advance

[edgar-manukyan]

Thanks team. Shall we add a new issue with Ramiro's nice findings/suggestions and refactor the derive_blfl in that issue?

[ShiyuC]

Hi @ShiyuC:

When it comes to this PR specifically, I think that the changes are working as expected.

I took a look at the function code itself and there are a few things I personally think should be improved (but this might be addressed on a separate issue or not... I leave it up to you, Edgar and Ramm to decide)

• ISO 8601 formatted dates are being used as character and not as date-times on their own right. This means that date and time comparisons are being done lexicographically, which I find dangerous (even though I understand the measures taken at dtc_datepart() and dtc_timepart() to make sure the format is comparable).
• Using dplyr verbs (dplyr::mutate(), dplyr::na_if(), tidyr::drop_na()) to make code more readable here:

  bad_orres_rows <- is.na(ds_mod[[domain_prefixed_names["orres"]]]) |
  trimws(ds_mod[[domain_prefixed_names["orres"]]]) %in% c("ND", "NOT DONE", "")
  ds_mod <- ds_mod[!bad_orres_rows, ]

• I think there is a bug in line 355, var_tpt -> tpt

  con_col <- c(domain_prefixed_names[c("testcd", "dtc", "var_tpt")], "VISIT")

• Not that I think it makes a difference in the resulting computations, but it would be more human-readable, I would change sdtm_in to ds_mod:

   con_col <- con_col[con_col %in% names(sdtm_in)]

• Is the setting of <unspecified> something that is part of the SDTM standard?
• Replace rbind() with dplyr's equivalent
• Replace dplyr::arrange_at() with arrange() as the former is superseded.
• Replace the pattern get(domain_prefixed_names["tpt"]) by idiomatic rlang alternatives, e.g. !!rlang::sym(...) or {{...}}.

We can probably add these comments to issue #59

[ShiyuC]

Ram's comment: add example for baseline_timepoints