Add ADAL01 #116

edelarua · 2023-09-08T19:05:19Z

Work from #38 moved here due to repo restructuring since previous PR was created.

Closes #37

edelarua · 2023-09-08T19:07:47Z

After your refactor of ADAB in random.cdisc.data, the "treatment emergent status" data is no longer present in adab (see change here), and the ATACHAR variable is no longer present in adab (see change here). Consequently, the "Characterization Results", "Patient Treatment Emergent ADA Status", and "Patient Treatment Emergent NAb Status" columns can no longer be derived in this listing. How should we proceed?

I have commented out the broken parts of the code to create the listing for now, which generates ADAL01 without the four missing columns until this is fixed.

qiliu1013 · 2023-09-08T19:40:09Z

Hi @qiliu1013,

After your refactor of ADAB in random.cdisc.data, the "treatment emergent status" data is no longer present in adab (see change here), and the ATACHAR variable is no longer present in adab (see change here). Consequently, the "Characterization Results", "Patient Treatment Emergent ADA Status", and "Patient Treatment Emergent NAb Status" columns can no longer be derived in this listing. How should we proceed?

I have commented out the broken parts of the code to create the listing for now, which generates ADAL01 without the four missing columns until this is fixed.

I will be out of office for the upcoming week but if you have any questions please feel free to reach out to anyone on the SME team!

Hi @edelarua, no need to show "Characterization Results" and "Patient Treatment Emergent NAb Status" in the ADAL01. A the new standard specs, there were move into PARAM now. We don't need to consider them.
"Patient Treatment Emergent ADA Status" now was in PARAMCD = "ADASTAT1".

Did I answer all your questions?

Thanks,
Qi

edelarua · 2023-09-08T19:54:11Z

Did I answer all your questions?

To confirm - "Patient Treatment Emergent ADA Status" also no longer need to be considered, correct? If so then yes you answered all my questions, and the template should be ready for review! Thanks Qi!!

qiliu1013 · 2023-09-08T20:16:30Z

Did I answer all your questions?

To confirm - "Patient Treatment Emergent ADA Status" also no longer need to be considered, correct? If so then yes you answered all my questions, and the template should be ready for review! Thanks Qi!!

Sorry. Patient Treatment Emergent ADA Status is PARAMCD = "ADASTAT1". No need to consider "Patient Treatment Emergent NAb Status"

github-actions · 2023-09-08T20:25:33Z

Unit Tests Summary

    1 files 2 suites 1m 9s ⏱️
  26 tests 0 ✔️   26 💤 0 ❌
287 runs 0 ✔️ 287 💤 0 ❌

Results for commit f60e542.

♻️ This comment has been updated with latest results.

qiliu1013 · 2023-09-13T19:21:00Z

Hi @edelarua, can you please share the output with me? Thanks!

shajoezhu · 2023-09-18T22:39:56Z

hi @qiliu1013 , can you review the output at https://github.com/insightsengineering/tlg-catalog/pull/116/files#diff-800dcce08155543ad547403b286591745b8c15d6d35a7b4fec7dc33a51da067c please

edelarua · 2023-09-20T21:20:04Z

@qiliu1013 see a screenshot of the TLG-C output here:

qiliu1013 · 2023-09-20T21:34:49Z

package/tests/testthat/_snaps/adal01/markdown-snaps.md

+  # A tibble: 24 × 9
+     USUBJID               VISIT      ISTPT   NFRLT RES_ADA  TU_ADA RES_NAB  TU_NAB AVAL_pk
+     <lstng_ky>            <lstng_ky> <fct>   <dbl> <chr>    <chr>  <chr>    <chr>  <chr>  
+   1 AB12345-RUS-16-id-165 Day 2      24H        24 Negative N/A    NA       N/A    0.00   


@edelarua, do you know why AVAL_PK is 0.00? It should be some numbers or NA. RES_ADA and TU_ADA seems not matched to me. I checked the data, they were matched. Can you please take a look?

@qiliu1013 I believe those AVAL values were set to 0 in adpc in random.cdisc.data. I have added a line in to convert 0 values as well as NAs to "N/A" for this column.

book/listings/pharmacokinetic/adal01.qmd

shajoezhu · 2023-10-18T05:46:34Z

blocking this for the moment. It seems we need some refactoring in the rcd data again.

qiliu1013 · 2024-09-27T23:13:01Z

@shajoezhu and @edelarua, can you please let me know where to find the latest adal01 code? I didn't see it under 37_adal01 branch. Thanks!

github-actions · 2024-09-28T07:18:53Z

🎉 Thank you for your contribution! Before this PR can be accepted, we require that you all read and agree to our Contributor License Agreement.
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✅ (edelarua)[https://github.com/edelarua]
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shajoezhu · 2024-09-28T07:29:07Z

I have read the CLA Document and I hereby sign the CLA

qiliu1013 · 2024-09-28T07:31:55Z

I have read the CLA Document and I hereby sign the CLA

book/listings/pharmacokinetic/adal01.qmd

Signed-off-by: Joe Zhu <[email protected]>

shajoezhu

need to update snapshot

shajoezhu · 2024-09-28T08:37:59Z

hi @edelarua , could you update the snapshot, once insightsengineering/random.cdisc.data#317 is in please. Thanks!

shajoezhu · 2024-09-28T08:45:56Z

this is potentially blocked by insightsengineering/random.cdisc.data#319

edelarua · 2024-09-30T16:25:24Z

Snapshot has been updated.

edelarua added 2 commits September 8, 2023 15:04

Add ADAL01 - missing 4 columns

1f34733

Update tlg-c index

b573710

edelarua added the sme label Sep 8, 2023

edelarua mentioned this pull request Sep 8, 2023

Add ADAL01 #38

Closed

Revert index changes for now to avoid cluttering this PR

7500ccf

Remove unnecessary columns

3d5a5d9

Merge branch 'main' into 37_adal01@main

195d4ad

Melkiades requested a review from qiliu1013 September 13, 2023 14:48

Melkiades and others added 2 commits September 19, 2023 09:39

Merge branch 'main' into 37_adal01@main

dd18638

Merge branch 'main' into 37_adal01@main

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Merge branch 'main' into 37_adal01@main

f75239a

qiliu1013 reviewed Sep 20, 2023

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edelarua and others added 5 commits September 20, 2023 18:23

Comment out broken columns

1f047fe

Convert 0 AVAL_pk values to NA

1b12da8

Merge 1b12da8 into 41f1d79

0ba5d01

[skip actions] Restyle files

96ffa5d

Empty commit

f60e542

shajoezhu marked this pull request as draft October 18, 2023 05:46

Merge branch 'main' into 37_adal01@main

b93be66

Update adal01

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shajoezhu and others added 2 commits September 28, 2024 15:29

Merge branch 'main' into 37_adal01@main

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Remove comment out

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shajoezhu reviewed Sep 28, 2024

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Update book/listings/pharmacokinetic/adal01.qmd

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Signed-off-by: Joe Zhu <[email protected]>

shajoezhu marked this pull request as ready for review September 28, 2024 08:33

shajoezhu requested changes Sep 28, 2024

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[skip style] [skip vbump] Restyle files

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edelarua added 2 commits September 30, 2024 12:23

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Add ADAL01 #116

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Add ADAL01 #116

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