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RConsortium / submissions-pilot3-adam

Development repo for pilot3 submission to FDA - ADaM
https://rconsortium.github.io/submissions-pilot3-adam/
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Compose a document to explain the tlf-report.pdf process (libreoffice, etc. for the rtf-to-pdf efficacy and primary output conversions) #183

Open robertdevine opened 6 months ago

robertdevine commented 6 months ago

@bms63 , @laxamanaj - PR this week. thx.

laxamanaj commented 5 months ago

Hi, @robertdevine .

Any draft documentation you have on these steps. Once drafted I can help update any details. Let me know.

robertdevine commented 5 months ago

Hi @laxamanaj , yes, I'll issue the PR tomorrow (Friday) and assign you and @bms63 as reviewers. Thx.

robertdevine commented 5 months ago

@laxamanaj - attached is a draft of the steps. It's interesting - during August 2023 I used libreoffice soffice command in my sandbox. You appear to have used the r2rtf package in your sandbox. For consistency with pilot1, the libreoffice functions were selected. In any event the tlf-report.pdf can be generated programmatically in ~50 lines of code (using either). Thx.

PILOT3_ISSUE_183_DRAFT_PDF_KNIT_PROCESS_STEPS.txt

Pilot3 tlf-report.pdf Generation {DRAFT}

Generation of the tlf-report.pdf can be knit using ~50 lines of R programming. Pilot3 Team developed the programmatic process on August 11, 2023 leading up to the initial submission.

For the initial submission in August 2023, a manual process was selected in place of the programmatic process in order to be consistent with the Pilot 1 process using {libreoffice}. This DRAFT is provided to flesh out the steps.

For automation purposes, generation of the tlf-report.pdf by R program has seven sections:

[1]Title Section (Lines 1-10) [2]Note Section (Line 12) [3]/path setting Section (Lines 16-18) [4]Table 14-2.01 Summary of Demographic and Baseline Characteristics Section (Lines 20-26) [5]Table 14-3.01 Primary Endpoint Analysis: ADAS Cog (11) - Change from Baseline to Week 24 - LOCF Section (Lines 30-37) [6]Table 14-3.02 Primary Endpoint Analysis: Glucose (mmol/L) - Summary at Week 20 - LOCF Section (Lines 41-44) [7]Figure 14-1 Time to Dermatologic Event by Treatment Group Section (Lines 48-54)

The program runs in a few seconds with tlf-report.pdf output and displayed in the browser.

Notes: In the manual process with the soffice command (libreoffice Win/Lin) was used to generate a .pdf output for both Primary Outputs (.rtf/.out) and merged into the final TLF report. It should be noted that Merck provides an open source R package {r2rtf} which was also tested during Pilot3 for the format conversion steps used to generate the tlf-report.pdf.

laxamanaj commented 5 months ago

Thanks for these notes, @robertdevine . For this re-submission, I couldn't get your automated steps to work on my end, so I ended going a manual route.

Do you mind joining our next available Thursday meeting so that you can demo these steps for me/us? I'm really curious how it worked on your end. I downloaded LibreOffice on my local computer and tried to run this in my local R, but I still couldn't get it to work. Hoping you can meet with me sometime. I'd appreciate it.

robertdevine commented 5 months ago

Will do, @laxamanaj. The next available Thursday meeting I'll jump on the call and run a quick demo. Pretty cool to see. [Getting ready to push the SAP item and call it a week.] Thanks again.

laxamanaj commented 5 months ago

Great. Thanks, @robertdevine . Our next meeting will actually be on the 30th of May as I'm not able to join next week. Hope that's ok with you.

robertdevine commented 5 months ago

Thanks @laxamanaj, Will do, I'll plan for 30th of May meeting for the demo.

@laxamanaj - I will also upload a video to show the programmatic run, similar to earlier ADRG videos from July/August 2023. Thx.

laxamanaj commented 5 months ago

@robertdevine . will you be joining the call today?

bms63 commented 5 months ago

@laxamanaj - attached is a draft of the steps. It's interesting - during August 2023 I used libreoffice soffice command in my sandbox. You appear to have used the r2rtf package in your sandbox. For consistency with pilot1, the libreoffice functions were selected. In any event the tlf-report.pdf can be generated programmatically in ~50 lines of code (using either). Thx.

PILOT3_ISSUE_183_DRAFT_PDF_KNIT_PROCESS_STEPS.txt

Pilot3 tlf-report.pdf Generation {DRAFT}

Generation of the tlf-report.pdf can be knit using ~50 lines of R programming. Pilot3 Team developed the programmatic process on August 11, 2023 leading up to the initial submission.

For the initial submission in August 2023, a manual process was selected in place of the programmatic process in order to be consistent with the Pilot 1 process using {libreoffice}. This DRAFT is provided to flesh out the steps.

For automation purposes, generation of the tlf-report.pdf by R program has seven sections:

[1]Title Section (Lines 1-10) [2]Note Section (Line 12) [3]/path setting Section (Lines 16-18) [4]Table 14-2.01 Summary of Demographic and Baseline Characteristics Section (Lines 20-26) [5]Table 14-3.01 Primary Endpoint Analysis: ADAS Cog (11) - Change from Baseline to Week 24 - LOCF Section (Lines 30-37) [6]Table 14-3.02 Primary Endpoint Analysis: Glucose (mmol/L) - Summary at Week 20 - LOCF Section (Lines 41-44) [7]Figure 14-1 Time to Dermatologic Event by Treatment Group Section (Lines 48-54)

The program runs in a few seconds with tlf-report.pdf output and displayed in the browser.

Notes: In the manual process with the soffice command (libreoffice Win/Lin) was used to generate a .pdf output for both Primary Outputs (.rtf/.out) and merged into the final TLF report. It should be noted that Merck provides an open source R package {r2rtf} which was also tested during Pilot3 for the format conversion steps used to generate the tlf-report.pdf.

Hey @robertdevine could this go into our wiki https://github.com/RConsortium/submissions-pilot3-adam/wiki in case we need to reproduce for another pilot?