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SwissClinicalTrialOrganisation / secuTrialR

Handling of data from the clinical data management system secuTrial
https://swissclinicaltrialorganisation.github.io/secuTrialR/
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mnpaid is mnppsd in German version resulting in missing Add-ID #235

Closed miljukov-o closed 3 years ago

miljukov-o commented 3 years ago

If I'm correct, in the German set-up of the ExportSearchTool (trial in German), mnpaid is exported as mnpsd, resulting in missing Add-ID, unfortunately blocking the use of read_validation_overview.

https://github.com/SwissClinicalTrialOrganisation/secuTrialR/blob/fb551f60dee4a2e3fa6e769e128b82bdfc741f9e/R/read_secuTrial_raw.R#L86

PatrickRWright commented 3 years ago

Hi @miljukov-o read_validation_overview() is intended to read data from the validation report into R. The validation report is not retrieved via ExportSearchTool though, so maybe there is a misunderstanding here. You retrieve the validation report from the Reports section in DataCapture.

Also mnpaid being mnpsd in the German version doesn't ring any bell for me. Maybe you can give a little more context or even an example export?

miljukov-o commented 3 years ago

Dear @PatrickRWright thank you very much for your reply. read_validation_overview() was just an example, where a missing mnpaid causes problems.

I have to correct: I meant mnppsd not mnpsd.

If I rename the column mnppsd to mnpaid in the casenode csv file in my exported zip-file and then read that zip file into R, then there is no problem and I can use the function form_status_summary(), which doesn't rely on additional report files (correct?).

PatrickRWright commented 3 years ago

If you need to change things manually in the export I wouldn't be too sure that everything is working as expected/designed so this would not be my approach of choice. Also, the mnppsd is definitely not the mnpaid. I had a quick look into the secuTrial manuals and found the following description for mnppsd:

mnppsd, Patient pseudonym, The random patient pesudonym. This identifier may not be exported.

The fact that it "may not be exported" confuses me a little since you seem to have an export containing it. In any case, I don't think this is related to the export language but rather to the export options more generally. Can you export the "Add-ID"? If you can and have not configured the ExportSearchTool to export it, then I suggest doing this which will likely solve your issue. If you can't export the "Add-ID" then I'm not sure I will be able to help you quickly since this may require some more extensive additions to secuTrialR.

PatrickRWright commented 3 years ago

I assume this is resolved.