Closes #14: ADTTE + ADRS with PFS examples

[DavidBlairs]

Pull Request

Howdy. I've had a go at writing up the examples for ADRS and ADTTE with PFS parameters. I think the ADTTE is a good draft (barring any amendment suggestions) but I'm thinking the ADRS article isn't sufficient just yet.

I was able to get a lot of information about ADTTE with PFS in the vignette provided here. However, there was nothing specifically relating to add PFS parameters in the basic ADRS vignette or in the more detailed version. I'd appreciate any assistance on this as well as any criticism on the ADRS example.

@rossfarrugia I added my name in the DESCRIPTION file in another PR, hence why you won't find it here.

• Title: Place Closes #<insert_issue_number> at the beginning of your PR title. Use the Edit button in the top-right if you need to update.
• Linked Issue: Ensure the related issue is linked in the "Development Section" on the right-hand side.
• First Contribution: If this is your first contribution, add yourself to the DESCRIPTION file.
• Impact on Examples: If your updates impact any examples, review locally for warnings or errors in the impacted example pages.
• Merge Conflicts: Developers should address any merge conflicts and merge upon successful review.
• New Packages: If new packages were used, ensure they are included in the DESCRIPTION file's Imports section.
• Updated Examples: If you added or updated an example, ensure it runs on the latest CRAN release versions of all packages used.
• Testing Instructions: Provide instructions on how to test the code if necessary.

[rossfarrugia]

thanks @DavidBlairs - will try and take a look over the next week when get chance and sure i could help advise for any gaps.

[DavidBlairs]

Hello @rossfarrugia. Can I just clarify, when the issue says "ADRS and ADTTE with minimal PFS parameters" does that mean:

1. create a minimal ADRS, then use the ADRS to create a minimal ADTTE and add PFS parameters
2. or does it mean create an ADRS with minimal PFS parameters and create an ADTTE with minimal PFS parameters

[rossfarrugia]

@DavidBlairs probably option 2 is easiest as you can use the pharmaverseadam adrs_onco as input to your ADTTE example as chances are you may need more than the brief example you create here for ADRS and saves you having to save the final dataset in this repo to be re-used in your ADTTE example.

[DavidBlairs]

@DavidBlairs probably option 2 is easiest as you can use the pharmaverseadam adrs_onco as input to your ADTTE example as chances are you may need more than the brief example you create here for ADRS and saves you having to save the final dataset in this repo to be re-used in your ADTTE example.

Debatably, given that the ADRS vignettes don't describe how to add PFS parameters specifically for ADRS, I'd say its easier to have one article thats ADRS -> ADTTE w/ PFS in terms of the documentation available. I'm just not sure if thats acceptable for #14

[rossfarrugia]

@DavidBlairs not sure i understand your point on the ADRS vignette - it shows here how to create disease progression parameter and here how to create death parameter, and these 2 then feed into ADTTE to create the PFS parameter.

I haven't had chance to review your PR yet sorry so in case it helps to further clarify here, i was imaging an ADRS example including a disease progression parameter and death parameter, and then an ADTTE example including a PFS parameter using these 2 from an ADRS.

[DavidBlairs]

@rossfarrugia that makes more sense. My confusion came from there not being anything specific in the ADRS vignette saying "PFS". Hold off on the review till next week, I'll give this a better go.

[DavidBlairs]

@rossfarrugia I think this is in a good place to receive critique. I look forward to your feedback

[rossfarrugia]

@DavidBlairs thanks for the first draft of these! i made some suggestions from an initial review of mainly the ADRS example. if you could make updates consistently across both then i'd be able to take another look and will spend a bit more time next review on ADTTE. let me know if any of my suggested updates are unclear as to why needed.

[DavidBlairs]

Hello @rossfarrugia. I added these amendments and did a larger rewrite to ensure ADTTE and ADRS were consistent with the ADaM guides already on the examples website. Let me know what you think.

[rossfarrugia]

thanks @DavidBlairs - will try find time over next few weeks to take another look

[rossfarrugia]

@DavidBlairs sorry it took me so long to get back around to this. thanks for all the updates! here's some more review comments for consideration.

[f-meister]

Hello @rossfarrugia I've made the changes you suggested and fixed up some issues with the spec. When you have the time, please go through these changes and let me know if I got the assignment right 😃

[rossfarrugia]

@f-meister one more thing needed is to follow this guidance from the README: https://github.com/pharmaverse/examples#scripts. Once you've done that and made the minor update requested above then i'm going to merge this and if anything else needs fixing i can take it. The CI fail is not related to your examples, so might have to dig into that one if it breaks when in main. I'm wondering if for some reason it's because this one is forked from our repo.