Part 2: Let's go! More ADaMs and more TLFs

[bms63]

@RConsortium/pilot5

Alright the promised issue for discussion on Part 2

• New Datasets (ADVS, ADMH, ADLBx, Efficacy?, Hy's Law)
• New Tables (AE Tables)
• New Figures (Volcano Plot, Tornados, something pretty)
• ARDs
• Shiny

I think a reading of the original SAP is order.

We have to get the FDA to be okay with this as they might not be able to review extra content.

[bms63]

If you have thoughts or ideas please share!!

I liked @SHAESEN2 idea on all the Tables matching the same style and format. Will really help with long-term maintenance!!

[SHAESEN2]

For ADaMs, I would suggest those mentioned in the ADRG. There are only few more:

• ADVS
• ADCIBC
• ADLBHY (and other ADLB although we can probably create one overall)
• ADNPIX

It seems CDISC removed the original content of the pilot. Now we only have one TLF program available on the link: https://github.com/cdisc-org/sdtm-adam-pilot-project
However, some of the outputs were regenerated by Atorus: https://github.com/atorus-research/CDISC_pilot_replication?tab=readme-ov-file

[bms63]

@SHAESEN2 can you link the ADRG here?

I think ADVS is a quick win for us as it is mostly coded here - https://pharmaverse.github.io/examples/adam/advs.html

Is there an easy way to read those rtfs from Atorus? It is nice there is some code that we can take a look at!

[robertdevine]

@RConsortium/pilot5, @bms63, @SHAESEN2 - the archived (safety and efficacy) datasets from the original SAP are available in the CDISC archive here. During Pilot 3 we used the Atorus pilot replication data for scientific purposes.

Worth consideration for p5 Part 2 would be an automated generation of formal conformance reporting with verified ADaM datasets - which may also compel further agency value for eCTD submission / information request(s) around p5.

[bms63]

@tataphani

Please check out this link for the code and outputs from the original Pilot. https://github.com/atorus-research/CDISC_pilot_replication?tab=readme-ov-file

The list that @robertdevine with the datasets is handy.

ADVS strikes me as easy win. Can you find a few examples of the code/outputs using ADVS so that we can discuss at Friday's meeting?

I think the next should be one of the ADQS--- datasets and related code/outputs but lets just go easy wins first!

[bms63]

Hi @tataphani - seeing if you have identified any outputs that might be fun for us to create in Part 2 of Pilot 5?

[tataphani]

PROGRAM Name | Datasets Used

t-14-1-01.R | ADSL
t-14-1.02 | ADSL
t-14-1-03.R | ADSL
t-14-2-01.R | ADSL
t-14-3-01.R | adas
t-14-3-02.R | adcibc.xpt
t-14-3-03.R | adadas.xpt
t-14-3-02.R | adcibc.xpt
t-14-3-05.R | adadas.xpt
t-14-3-06.R | adcibc.xpt
t-14-3-07.R | adadas.xpt
t-14-3-08.R | adadas.xpt
t-14-3-09.R | adadas.xpt
t-14-3-09.R | adadas.xpt
t-14-3-11.R | adadas.xpt
t-14-3-12.R | adnpix.xpt
t-14-3-13.R | adcibc.xpt
t-14-4-01.R | adsl.xpt
t-14-5-01.R | adae.xpt
t-14-5-02.R | adae.xpt
t-14-6-01.R | adlbc.xpt
t-14-6.02 | adlbc.xpt
t-14-6.03 | adlbcpv adlbc.xpt
T-14-6.04 | adlbc.xpt adlbh.xpt
T-14-6.05 | adlbc.xpt adlbh.xpt
14-6.06 | adlbhy
T-14-7.01 | advs.xpt
T-14-7.02 | advs.xpt ADSL
T-14-7.03 | advs
t-14-7.01 | ADSL cm.xpt
 

[tataphani]

List.xlsx - table_na.csv

[bms63]

Thanks @tataphani!! no need to close as ongoing discussion

FYI @RConsortium/pilot5