Add get_surv_times_df and get_surv_diff_df()/ overhaul creation of survival times tables #269
Open
jszczypinski wants to merge 18 commits into
Open
Add get_surv_times_df and get_surv_diff_df()/ overhaul creation of survival times tables #269jszczypinski wants to merge 18 commits into
jszczypinski wants to merge 18 commits into
Conversation
**What changes are proposed in this pull request?** * `tbl_survfit_quantiles()` now indicates censored observation in min/max values with `*` (#192) Small change as requested in the issue below: Censored min/max range values are now marked with `*` Closes #192 -------------------------------------------------------------------------------- Pre-review Checklist (if item does not apply, mark is as complete) - [ ] **All** GitHub Action workflows pass with a ✅ - [ ] PR branch has pulled the most recent updates from master branch: `usethis::pr_merge_main()` - [ ] If a bug was fixed, a unit test was added. - [ ] Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): `devtools::test_coverage()` - [ ] Request a reviewer Reviewer Checklist (if item does not apply, mark is as complete) - [ ] If a bug was fixed, a unit test was added. - [ ] Run `pkgdown::build_site()`. Check the R console for errors, and review the rendered website. - [ ] Code coverage is suitable for any new functions/features: `devtools::test_coverage()` When the branch is ready to be merged: - [ ] Update `NEWS.md` with the changes from this pull request under the heading "`# cards (development version)`". If there is an issue associated with the pull request, reference it in parentheses at the end update (see `NEWS.md` for examples). - [ ] **All** GitHub Action workflows pass with a ✅ - [ ] Approve Pull Request - [ ] Merge the PR. Please use "Squash and merge" or "Rebase and merge".
This reverts commit b610804.
This reverts commit 382610f.
Contributor
Unit Tests Summary 1 files 263 suites 3m 54s ⏱️ Results for commit 0fc082a. ♻️ This comment has been updated with latest results. |
Contributor
Unit Test Performance Difference
Additional test case details
Results for commit b726237 ♻️ This comment has been updated with latest results. |
Contributor
|
Code Coverage SummaryDiff against mainResults for commit: 0fc082a Minimum allowed coverage is ♻️ This comment has been updated with latest results |
Melkiades
reviewed
Jun 18, 2026
Comment on lines
+40
to
+43
| get_surv_times_df <- function(fit_km, times, conf_int = 0.95, scale = 1) { | ||
| # Enforce rigorous type-checking using rlang | ||
| if (!inherits(fit_km, "survfit")) { | ||
| rlang::abort("`fit_km` must be a survfit object.") |
Contributor
There was a problem hiding this comment.
I like it a lot!!! I think it is an amazing way forwards. Just wondering if the two get_* could be in the tbl_survfit_times. Just wondering because if they are only used there that would make documentation a bit more compact and direct (I know I have asked differently for helper functions in the past but these are exported and used only there right?)
Contributor
There was a problem hiding this comment.
I will do the full review tomorrow! ;)
jszczypinski
changed the title
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This PR overhauls the survival time summary pipeline, shifting from a tightly coupled architecture to a modular two-step process (Data Extraction ➔ Presentation). This mirrors tbl_coxph() and empowers users to manipulate summary contents via standard dplyr wrangling before rendering tables or plotting annotations.
🚀 New Extraction Engine
get_surv_times_df(): A new function to extract survival metrics, numbers at risk, and CIs into a highly malleable data.frame.
get_surv_diff_df(): Added a companion extractor leveraging cardx to calculate pairwise survival differences, complete with CIs and p-values.
🎨 Presentation & Rendering
tbl_survfit_times(): Refactored to process structured data frames rather than raw survfit models. Automatically maps dynamically bound columns (like the p-value output from get_surv_diff_df()).
annotate_surv_med(): Updated the function signature to accept a pre-computed data frame (surv_tbl), acting as a generic floating table renderer identical to annotate_coxph().
🛑 Legacy Migration & Fixes
Defunct Methods: Made add_overall() and add_difference_row() defunct for tbl_survfit_times. They now throw explicit errors guiding users to extract data and use the dplyr::bind_rows() workflow instead.
Strict Type Safety: Resolved vctrs/bind_rows() crashes by ensuring empty columns map correctly to NA_real_ across extractors.
Documentation Clean-up: Fixed Roxygen2 parameter mismatches and rewrote @examples to demonstrate advanced configuration scenarios.
Closes #268
Pre-review Checklist (if item does not apply, mark is as complete)
usethis::pr_merge_main()devtools::test_coverage()Reviewer Checklist (if item does not apply, mark is as complete)
pkgdown::build_site(). Check the R console for errors, and review the rendered website.devtools::test_coverage()When the branch is ready to be merged:
NEWS.mdwith the changes from this pull request under the heading "# cards (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (seeNEWS.mdfor examples).