Add test case for baseline_timepoints in derive_blfl function

[ShiyuC]

This PR touches #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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[github-actions]

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

[ShiyuC]

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

[ramiromagno]

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• Replace dplyr::arrange_at() with arrange() as the former is superseded.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 {{...}}.

[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

[ShiyuC]

• 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).
  Confirmed that ISO 8601 will be applied to date time variables before blfl derivation, so comparing in lexicographic order should be fine. I will add code in there to check the format and give message
• Is the setting of something that is part of the SDTM standard?
  This is not SDTM standard, but we fill in the value to make sure VISIT does not have blank values.