82 adlbc derivations

[nicolekjones]

Hi all,

I did a bit of cleaning of the code

• there was an udpate to the adlbc ADT derivatoin chaingin vars() to exprs() which caused the program to break in my area
• ADTM was derived, but not used in final dataset so I removed derivation
• added @DadongZ 's fix for calculating maxALBTRVAL for AENTMTFL

Specs were updated

• I removed any other ADLB datasets
• Updated origins and provided predecessors, methods and verified the codelists
• It would be great to have one more set of eyes to make sure I'm following this correctly

[laxamanaj]

Hi, @nicolekjones . Many thanks for this update and appreciate your flexibility to check on your code and adapt to the updated R environment. One thing I noticed in this PR is that there is a conflict with the specs being used. We did merge a new set of specs from #90 which should be in main now. I just wanted to make sure you did this :

git checkout main
git pull
git checkout [your branch]
git merge --no-edit main

then run renv::restore() in console

Before you made the update to the ADLBC specs above?

[nicolekjones]

Hi, @nicolekjones . Many thanks for this update and appreciate your flexibility to check on your code and adapt to the updated R environment. One thing I noticed in this PR is that there is a conflict with the specs being used. We did merge a new set of specs from #90 which should be in main now. I just wanted to make sure you did this :

git checkout main
git pull
git checkout [your branch]
git merge --no-edit main

then run renv::restore() in console

Before you made the update to the ADLBC specs above?

I thin i missed that last step. I did:

git checkout main
git pull main
git checkout -b

I believe there was a merge that happened between creating the branch and my final push I’ll resolve this afternoon 😁

[laxamanaj]

Hi, @nicolekjones . Many thanks for this update and appreciate your flexibility to check on your code and adapt to the updated R environment. One thing I noticed in this PR is that there is a conflict with the specs being used. We did merge a new set of specs from #90 which should be in main now. I just wanted to make sure you did this :

git checkout main
git pull
git checkout [your branch]
git merge --no-edit main

then run renv::restore() in console

Before you made the update to the ADLBC specs above?

I thin i missed that last step. I did:

git checkout main git pull main git checkout -b

I believe there was a merge that happened between creating the branch and my final push I’ll resolve this afternoon 😁

Thanks, @nicolekjones . I see now the bumps we can run into with the git workflow. I'm still learning myself. :)

[nicolekjones]

@laxamanaj Looks like I resolved merge conflict! Checks are running. If any have issue I'll resolve after they finish.

I think merge conflicts are often part of the journey.
I think we've done a good job so far :)

[laxamanaj]

Hi, @nicolekjones . Thanks for the PR. I've added some comments for lines 198 and 244. Best,
Joel

[nicolekjones]

@laxamanaj, just pushed the updates. For those full_joins yes we do expect a one to many merge. updated so the warning is suppressed!

[laxamanaj]

Hi, @nicolekjones . I have one more comment regarding lines 36-40.

[laxamanaj]

Hi, @nicolekjones . Thanks for all of your help on making these updates. Apologes, one last thing, I believe we should update. After reviewing the code, I see lines 36-40 seem to depend on the CDISCPlot01 adam/ADLBC. Can we remove this if not needed as to not confuse FDA why we are reading another version of ADLBC?

## Analysis Dataset Lab Blood Chemistry
prodc <- convert_blanks_to_na(read_xpt(file.path("adam", "adlbc.xpt")))

# Variables for programming
toprogram <- setdiff(colnames(prodc), c(colnames(lb), unique(supplb[["QNAM"]])))

[nicolekjones]

Sure! I think we put this in initially to see what was needed, but you're right we don't need it.

After running metacore I am getting these warnings

Metadata successfully imported
Warning messages:
1: core from the ds_vars table only contain missing values.

supp_flag from the ds_vars table only contain missing values.

dataset from the supp table only contain missing values.

variable from the supp table only contain missing values.

idvar from the supp table only contain missing values.

qeval from the supp table only contain missing values.

 
2: The following variables are in the ds_vars table, but don't have value specs:
 ADLBC.AVAL, ADTTE.AVAL 

 
3: The following derivations are never used:
 ADLBC.ABLFL: Y if VISITNUM=1, null otherwise
 ADLBC.AGE: ADSL.AGE
 ADLBC.AGEGR1: ADSL.AGEGR1
 ADLBC.AGEGR1N: ADSL.AGEGR1N
 ADLBC.AVAL: LB.LBSTRESN
 ADLBC.COMP24FL: ADSL.COMP24FL
 ADLBC.DSRAEFL: ADSL.DSRAEFL
 ADLBC.LBNRIND: LB.LBNRIND
 ADLBC.LBSEQ: LB.LBSEQ
 ADLBC.LBSTRESN: LB.LBSTRESN
 ADLBC.PARAMCD: LBTESTCD
 ADLBC.RACE: ADSL.RACE
 ADLBC.RACEN: ADSL.RACEN
 ADLBC.SAFFL: ADSL.SAFFL
 ADLBC.SEX: ADSL.SEX
 ADLBC.STUDYID: ADSL.STUDYID
 ADLBC.SUBJID: ADSL.SUBJID
 ADTTE.AVAL: ADT-STARTDT+1 

 
4: The following codelist(s) are never used:
 Medical Dictionary for Regulatory Activities 

I'm not 100% sure how to resolve these or if it's a concern. I'm also not sure why ADTTE.AVAL is showing up here .
It appears to be from variables that all are predecessors. I noticed that other datasets provided a derivation in the Methods for variables like AGE despite them being predecessors, so I followed that practice. Do you think I should remove predecessors from Methods tab?

[laxamanaj]

Thanks for notifying me of the metacore spec issues. This can be fixed.

Essentially the way the specs work, only should a variable be included in the Methods tab, if in the Variables tab Origin='Derived'. Otherwise, if Origin='Predecessor', then the variable should not be in the Methods tab.

So for example, for ADLBC.AGE, this warning is saying that this derivation has never been used, because in the Variables tab for ADLBC.AGE, it is set to Predecessor, but if it was set to Derived it will be ok to keep in the Methods tab. So there are 2 ways to fix it.

1. In the Variables tab, for this example, you can set ADLBC.AGE to Origin='Derived' & Method='ADLBC.AGE' (this will be the corresponding ID in the Methods tab). Then in the Methods tab, leave the row ADLBC.AGE as-is.

2. In the Variables tab, for this example, you can leave ADLBC.AGE set to Origin='Predecessor', then in the Methods tab , delete/remove the row ADLBC.AGE, since it is not identified as Origin='Derived'. This approach answers your original question.

Similar approach should be taken for the rest of the variables in this warning, this will then fix bullet 3.

I hope this makes sense. Let me know if you want discuss in meeting also. Happy to do so.

Finally, once the warning in bullet 3 are resolved, then the other warnings can be left as-is and you can add the argument quiet=T, which will then mute these warnings in the run. For example : metacore <- spec_to_metacore("adam/TDF_ADaM - Pilot 3 Team updated.xlsx", where_sep_sheet = FALSE, quiet = T)

As for why ADTTE.AVAL is showing up here, I'm not sure as the Variables tab and Methods tab seem be set accordingly. @bms63 or @DeclanHodges , wondering if you may have some insight on this on the GSK side of this?

[nicolekjones]

makes sense! I was under the impression that predecessors shouldn't have entries in the methods tab, but I thought maybe I was wrong. Removed them and added the quiet = true.

I was wondering the same thing with adtte.aval. I looks fine and when I check, there's no link between ADTTE and ADLBC.

Let me know if I need to make any further changes!

[laxamanaj]

Many thanks for these swift updates, @nicolekjones . I will merge now.