@bundfussr@bms63 please take a look at the JSON file, I have put each line of the case statement in a variable, so JSON file more readable. I then just concatenate them together and put a case statement around it in scriptatoxgr_sources.
So we would have a JSON file for each set of criteria. Let me know what you think, and then I can do the rest, including NCICTCAEv6.

@bundfussr@bms63 thanks for initial input. I will get JSON files created for existing criteria we have, can maybe have a further QC then. I will then work on NCICTCAEv6, once current criteria organised.
@bms63 regarding the work around handling the JSON files, can I leave that to you, to create appropriate tickets, as this can be an additional, separate piece of work.
I have found editting the JSON files directly quite easy, for ERRORs found I just updated the JSON file, I didn't go back to the xlslx file for edits.

@bms63@bundfussr@manciniedoardo the criteria for CREATININE INCREASED in NCICTCAEv6 causes a slight issue with how we have things set up currently.
For Grade 2 we have the following (its similar for grade 3).

>1.5 - 3.0 x if baseline is below LLN; >1.5 - 3.0 x ULN

This is to createATOXGRH derivation, so we would normally pass in "H" or "HIGH" for the input parameterabnormal_indicator, as normally for ATOXGRH we would look atupper limit of normal (and for ATOXGRL we would look atlower limit of normal).

So we need a way to pass in value of "L" or "LOW" to checkBNRIND against for ATOXGRH.

For me the easiest way to do this, is to replace the argumentabnormal_indicator inderive_var_atoxgr_dir with 2 arguments,low_indicator andhigh_indicator, but this would break backward compatibility.
The change is only required if you are using NCICTCAEv6 criteria.

Maybe worth a discusssion at one of our regular meetings?

@bms63@bundfussr@manciniedoardo the criteria for CREATININE INCREASED in NCICTCAEv6 causes a slight issue with how we have things set up currently. For Grade 2 we have the following (its similar for grade 3).

>1.5 - 3.0 x if baseline is below LLN; >1.5 - 3.0 x ULN

This is to createATOXGRH derivation, so we would normally pass in "H" or "HIGH" for the input parameterabnormal_indicator, as normally for ATOXGRH we would look atupper limit of normal (and for ATOXGRL we would look atlower limit of normal).

So we need a way to pass in value of "L" or "LOW" to checkBNRIND against for ATOXGRH.

For me the easiest way to do this, is to replace the argumentabnormal_indicator inderive_var_atoxgr_dir with 2 arguments,low_indicator andhigh_indicator, but this would break backward compatibility. The change is only required if you are using NCICTCAEv6 criteria.

Maybe worth a discusssion at one of our regular meetings?

Discussion from this week's call: team agrees with the breaking change as proposed by@millerg23, especially as the deprecation cycle is quite slow now so the impact will be reduced in the short-medium term. Lab grading vignette should also be updated to explain that this is relevant for v6 only.

What an epic PR@millerg23 !! Looking good.

What are you think for the news? We have deprecation, new ctcae info, json as a backbone, possible lab vignette and more!?!? woooo!!

Hey@millerg23 - do you think we can finish this one up soon?

@bms63@manciniedoardo I updated lab grading Vignette, would be great of you could review. I also noticed I had missed "Creatinine Clearance decreased", which I have now added. For this lab test I have set grade to be missing when AVAL < 10, I have asked our lab experts in Roche if this is most conservative approach, it doesn't seem right set it to zero when its clearly a very abnormal result.
@bms63 I need to update the NEWS page, but if you want to do it, please go ahead, you will make it sound more grand than me!! Not a problem though if you don't have time.

@copilot can you make a grandiose news item for News.md following the News.md convention summarizing the awesomeness of this PR.

@bms63 I've opened a new pull request,#2914, to work on those changes. Once the pull request is ready, I'll request review from you.

@bms63@manciniedoardo@bundfussr did we agree to update ADLB template script to use NCICTCAEv5 instead of NCICTCAEv4? As currently for NCICTCTAEv4 we don't need the input parametershigh_indicator,low_indicator (or previouslyabnormal indicator

@bms63@manciniedoardo@bundfussr did we agree to update ADLB template script to use NCICTCAEv5 instead of NCICTCAEv4? As currently for NCICTCTAEv4 we don't need the input parametershigh_indicator,low_indicator (or previouslyabnormal indicator

from memory we said we'd at least write a comment saying that if you're using version x, you have to make the following changes/use the following arguments etc.

@bms63@manciniedoardo@bundfussr did we agree to update ADLB template script to use NCICTCAEv5 instead of NCICTCAEv4? As currently for NCICTCTAEv4 we don't need the input parametershigh_indicator,low_indicator (or previouslyabnormal indicator

from memory we said we'd at least write a comment saying that if you're using version x, you have to make the following changes/use the following arguments etc.

Added a comment in the ADLB template script, also added a bit about Creatinine Increased in Grading Vignette, as this usesBNRIND also.
Let me know if any other updates required.

I think most of my comments were minor - I'm not super aware of Lab stuff. Should we ask a Lab person to take a look from Roche or GSK to take a look? Probably not the best time with the holidays.