ADaM example for ADVS and update ADSL (as being used for upcoming R/Pharma workshop)

[rossfarrugia]

GOAL: Using updated code and specs from R/Pharma 2024 Workshop - rework the ADSL example and add in the ADVS example

@rossfarrugia @jeffreyad what do you think about combining the specs at at least for ADSL, ADVS, ADPC, ADPPK? Maybe the oncology could get added in as well?

[bms63]

@Fanny-Gautier I am happy to work on this, but wondering if you would like to take it on? Put those quarto skills to use! :)

[rossfarrugia]

thanks @bms63 - i have no strong preference about the specs, i thought keeping them separate makes it easier if different individuals wanted to work on these in parallel, and also it opens up to all kinds of different types of ADaM specs people might use so as to show how flexible {metacore} can be.

[bms63]

i might just combine ADSL, ADVS ADPC and ADPPK so the specs are a little richer.

[jeffreyad]

Yes, go ahead and combine them. That sounds good to me

[Fanny-Gautier]

1. @bms63 Could you please assign me to this issue as well ? Thanks.

2. For the specs should I create new specs combining ADSL, ADVS, ADPC, and ADPPK? or should I rename the current PK specs and add ADSL and ADVS?
   Should I also add the Methods knowing that our examples during the R/Pharma Workshop didn't always followed the ADaM IG or are not real derivations?

3. To work on pharmaverse/exemples, I need to create a fork from my end, right ?

[rossfarrugia]

@Fanny-Gautier i gave you repo write access now so you can make a branch here directly, instead of needing to fork. I leave Ben to answer the other question

[bms63]

1. @bms63 Could you please assign me to this issue as well ? Thanks.
2. For the specs should I create new specs combining ADSL, ADVS, ADPC, and ADPPK? or should I rename the current PK specs and add ADSL and ADVS?

I think we should combine the 4. However you do it is fine just shouldn't impact the ADPC and ADPPK!

Should I also add the Methods knowing that our examples during the R/Pharma Workshop didn't always followed the ADaM IG or are not real derivations?

Adding the Methods is nice - I can help update the specs to be "more correct" once this is further along. It helps later as nice to define the derivation that is being done and prevent later headaches like we are experiencing with ADEG derivations template

3. To work on pharmaverse/exemples, I need to create a fork from my end, right ?

[Fanny-Gautier]

Hi @bms63 ,
Could you please have a look at the current ADSL_ADVS_pk_spec, especially the codelist where I have maintained the initial format (e.g. Name column) as in the pk_spec. I am unfortunately not an expert yet on this part of ADaMs specs and I have the feeling that what we did for the Workshop was better.
Please let me know your comments. Many thanks

[Fanny-Gautier]

Please note that I currently have a system issue and I am unable to login to posit Workbench. I have raised a ticket this morning, and my IT is currently working on it ... so I can work on the specs part only for now.

[bms63]

Lets keep in the style of the workshop spec then. I thought they were identical :(