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pharmaverse / pharmaverseadam

Test ADaM data for use with pharmaverse
https://pharmaverse.github.io/pharmaverseadam
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[Feature Request] Missing variables in ADEG and ADEX #78

Open edelarua opened 2 months ago

edelarua commented 2 months ago

Hello again,

While testing safety templates in scda.test, we found that the following variables are missing from the ADEG and ADEX datasets:

If you require any further details please let me/the SME team know.

Thanks!

kaz462 commented 1 month ago

Hi @edelarua , thanks for the feature request! Could you please provide detailed derivations for ADEG.WORS02FL and ADEX.PARCAT2?

edelarua commented 1 month ago

Could you please provide detailed derivations for ADEG.WORS02FL and ADEX.PARCAT2?

Hi @kaz462,

WORS02FL has label "Worst Post-Baseline Observation" and is equal to "Y" when ABLFL != "Y" and grade/level is worst on a per-patient basis.

PARCAT2 has label "Parameter Category 2" and correlates with the ACTARM variable. It is described as "Name of Actual Treatment. Addtional identification information may be added to uniquely identify a study treatment, if necessary."

kaz462 commented 2 weeks ago

AVALU and WORS02FL won't be added to pharmaverseadam per discussion from https://github.com/pharmaverse/admiral/issues/2490

kaz462 commented 2 weeks ago

PARCAT2 has label "Parameter Category 2" and correlates with the ACTARM variable. It is described as "Name of Actual Treatment. Addtional identification information may be added to uniquely identify a study treatment, if necessary."

For PARCAT2, @edelarua could you please provide more details on what values need to be populated for each parameter?

e.g., we currently have PARCAT1 with the following values mapped to PARAM

> dplyr::count(adex, PARCAT1, PARAMCD, PARAM)
# A tibble: 19 × 4
   PARCAT1    PARAMCD PARAM                                                          n
   <chr>      <chr>   <chr>                                                      <int>
 1 INDIVIDUAL ADJ     Dose adjusted during constant dosing interval                591
 2 INDIVIDUAL ADJAE   Dose adjusted  due to AE during constant dosing interval     591
 3 INDIVIDUAL DOSE    Dose administered during constant dosing interval (mg)       591
 4 INDIVIDUAL DURD    Study drug duration during constant dosing interval (days)   591
 5 INDIVIDUAL PLDOSE  Planned dose during constant dosing interval (mg)            591
 6 OVERALL    AVDDSE  Average daily dose administered (mg/mg)                      254
 7 OVERALL    TADJ    Dose adjusted during study                                   254
 8 OVERALL    TADJAE  Dose adjusted during study due to AE                         254
 9 OVERALL    TDOSE   Total dose administered (mg)                                 254
10 OVERALL    TDOSINT Overall dose intensity (%)                                   254
11 OVERALL    TDURD   Overall duration (days)                                      254
12 OVERALL    TPDOSE  Total planned dose (mg)                                      254
13 WEEK 2-24  PADJ    Dose adjusted during W2-W24                                  226
14 WEEK 2-24  PADJAE  Dose adjusted  in W2-W24 due to AE                           226
15 WEEK 2-24  PAVDDSE Average daily dose administered in W2-W24 (mg)               226
16 WEEK 2-24  PDOSE   Total dose administered in W2-W2 (mg)4                       226
17 WEEK 2-24  PDOSINT W2-24 dose intensity (%)                                     226
18 WEEK 2-24  PDURD   Overall duration in W2-W24 (days)                            226
19 WEEK 2-24  PPDOSE  Total planned dose in W2-W24 (mg)                            226

Thanks!

edelarua commented 2 weeks ago

Hi @kaz462,

As an example, the PARCAT2 variable in our current dummy data has values "Drug A" and "Drug B". This variable is used for row-wise stratification of our tables, so the names of the levels are not particularly important.