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Closes #253 fix_bor_ne: Add CR and PR to bor_ne event #271

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merged 6 commits into from
Dec 13, 2023
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Closes #253 fix_bor_ne: Add CR and PR to bor_ne event #271

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7d74789
#253 fox_bor_ne: add CR and PR to bor_ne event
bundfussr Dec 13, 2023
243e588
Merge branch 'main' into 253_fix_bor_ne
bundfussr Dec 13, 2023
5ca324a
#253 fox_bor_ne: add NEWS item
bundfussr Dec 13, 2023
18e89c2
#253 fox_bor_ne: improve line breaks in PR template
bundfussr Dec 13, 2023
d583b38
#253 fix_bor_ne: add backticks
bundfussr Dec 13, 2023
dcea67f
#253 fix_bor_ne: update ibor_ne
bundfussr Dec 13, 2023
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12 changes: 2 additions & 10 deletions .github/pull_request_template.md
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@@ -1,14 +1,6 @@
Thank you for your Pull Request! We have developed this task checklist from the
[Development Process
Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html#detailed-development-process)
to help with the final steps of the process. Completing the below tasks helps to
ensure our reviewers can maximize their time on your code as well as making sure
the admiral codebase remains robust and consistent.
Thank you for your Pull Request! We have developed this task checklist from the [Development Process Guide](https://pharmaverse.github.io/admiral/CONTRIBUTING.html#detailed-development-process) to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.

Please check off each taskbox as an acknowledgment that you completed the task
or check off that it is not relevant to your Pull Request. This checklist is
part of the Github Action workflows and the Pull Request will not be merged into
the `main` branch until you have checked off each task.
Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the `main` branch until you have checked off each task.

- [ ] Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update). Then the issue is closed automatically once it is merged to `main`.
- [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/). Run `styler::style_file()` to style R and Rmd files
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7 changes: 7 additions & 0 deletions NEWS.md
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# admiralonco (development version)

## Updates of Existing Functions

- The `bor_ne` event object was updated such that `CR` and `PR` are additionally
considered as event. This ensures that the confirmed best overall response for a
patient with a single `CR` or `PR` assessment is derived as `"NE"` instead of
`"MISSING"`. (#253)

## Documentation

- New vignette "Creating ADRS with iRECIST endpoints". (#233)
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6 changes: 3 additions & 3 deletions R/response_sources.R
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Expand Up @@ -136,11 +136,11 @@ bor_pd <- event(
#' @export
bor_ne <- event(
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shouldn't this update be for cbor_ne rather than bor_ne? that's what we did for admiralroche.

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We do not have cbor_ne in admiralonco. We use bor_ne for both BOR and CBOR.

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Do you think we should change this?

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ok, happy to go with your call as I see similar case with bor_sd. i'll approve for now and then if you decide to update i can re-review.

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we should also update ibor_ne for iRECIST

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Good point.
Updated

description = paste(
"Define not evaluable (NE) for best overall response (BOR) as SD, NON-CR/NON-PD,",
"or NE (should be specified after bor_sd and bor_non_crpd)"
"Define not evaluable (NE) for best overall response (BOR) as CR, PR, SD,",
"NON-CR/NON-PD, or NE (should be specified after bor_sd and bor_non_crpd)"
),
dataset_name = "ovr",
condition = AVALC %in% c("SD", "NON-CR/NON-PD", "NE"),
condition = AVALC %in% c("CR", "PR", "SD", "NON-CR/NON-PD", "NE"),
set_values_to = exprs(AVALC = "NE")
)

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6 changes: 3 additions & 3 deletions vignettes/irecist.Rmd
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Expand Up @@ -648,11 +648,11 @@ ibor_iupd <- event(

ibor_ne <- event(
description = paste(
"Define not evaluable (NE) for best overall response (iBOR) as iSD, NON-iCR/NON-iUPD,",
"or NE (should be specified after ibor_isd and ibor_non_icriupd)"
"Define not evaluable (NE) for best overall response (iBOR) as iCR, iPR, iSD,",
"NON-iCR/NON-iUPD, or NE (should be specified after ibor_isd and ibor_non_icriupd)"
),
dataset_name = "ovr",
condition = AVALC %in% c("iSD", "NON-iCR/NON-iUPD", "NE"),
condition = AVALC %in% c("iCR", "iPR", "iSD", "NON-iCR/NON-iUPD", "NE"),
set_values_to = exprs(AVALC = "NE")
)

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