init commit #141

shajoezhu · 2025-11-28T05:48:03Z

What changes are proposed in this pull request?

Style this entry in a way that can be copied directly into NEWS.md. (#, @)

Provide more detail here as needed.

Reference GitHub issue associated with pull request. e.g., 'closes #'

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

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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).
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Merge the PR. Please use "Squash and merge" or "Rebase and merge".

shajoezhu · 2025-11-28T05:48:31Z

try and use exisitng structure and surv functions, refactoring will be addressed in #142

github-actions · 2025-11-28T05:52:05Z

Unit Tests Summary

1 files 69 suites 1m 27s ⏱️
69 tests 69 ✅ 0 💤 0 ❌
169 runs 169 ✅ 0 💤 0 ❌

Results for commit d5a79b7.

♻️ This comment has been updated with latest results.

github-actions · 2025-11-28T05:52:08Z

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
gkm	👶		$+0.03$	$+3$	$0$	$0$	$0$
modify_header_rm_md	💔	$0.11$	$+1.13$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
add_hierarchical_count_row	💔	$4.81$	$+1.13$	add_hierarchical_count_row_works
gkm	👶		$+0.03$	test_gkm_works
modify_header_rm_md	💔	$0.11$	$+1.13$	strip_md_bold_works_with_gtsummary_table

Results for commit b524fa0

♻️ This comment has been updated with latest results.

github-actions · 2025-11-28T05:52:37Z

Code Coverage Summary

Filename                               Stmts    Miss  Cover    Missing
-----------------------------------  -------  ------  -------  ----------------------------------------------------------------------------------------------------------------------
R/add_blank_rows.R                        63       0  100.00%
R/add_hierarchical_count_row.R            33       0  100.00%
R/crane-package.R                          2       2  0.00%    18-19
R/deprecated.R                             6       6  0.00%    15-21
R/gkm.R                                  330      54  83.64%   52, 107-124, 140, 204, 268, 291, 362-364, 368-375, 398-400, 407-410, 414, 425-429, 442, 444-446, 460, 463-467, 582-586
R/label_roche.R                           72       0  100.00%
R/modify_header_rm_md.R                   18       2  88.89%   35-36
R/modify_zero_recode.R                    13       0  100.00%
R/tbl_baseline_chg.R                     186       0  100.00%
R/tbl_hierarchical_rate_and_count.R      148       0  100.00%
R/tbl_hierarchical_rate_by_grade.R       271       3  98.89%   162-164
R/tbl_listing.R                           35       0  100.00%
R/tbl_null_report.R                        9       0  100.00%
R/tbl_roche_summary.R                     64       0  100.00%
R/tbl_shift.R                            116       0  100.00%
R/tbl_survfit_quantiles.R                132       1  99.24%   295
R/tbl_survfit_times.R                     92       0  100.00%
R/theme_gtsummary_roche.R                 74       0  100.00%
R/utils.R                                 36       0  100.00%
TOTAL                                   1700      68  96.00%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  -------
R/gkm.R        +330     +54  +83.64%
TOTAL          +330     +54  -2.98%

Results for commit: d5a79b7

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

shajoezhu · 2025-11-28T15:19:49Z

need examples and export
h_km_fit, h_tbl_coxph_pairwise,

…to adding_g_km

shajoezhu · 2025-11-30T02:54:15Z

my styler is failing, @edelarua , i was wondering how you guys check style here https://github.com/insightsengineering/crane/actions/runs/19792793759/job/56708402248?pr=141

shajoezhu · 2025-11-30T02:55:43Z

checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'annot_cox_ph.Rd':
‘control_coxph_annot’

Missing link(s) in Rd file 'annot_surv_med.Rd':
‘control_surv_med_annot’

Missing link(s) in Rd file 'h_tbl_coxph_pairwise.Rd':
‘control_coxph’

Missing link(s) in Rd file 's_coxph_pairwise.Rd':
‘control_coxph’

See section 'Cross-references' in the 'Writing R Extensions' manual.

checking for missing documentation entries ... WARNING
Undocumented code objects:
‘obj_label’
Undocumented S4 methods:
generic 'obj_label' and siglist 'ANY'
generic 'obj_label<-' and siglist 'ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'obj_label-set.Rd'
‘obj’

Melkiades · 2025-12-01T14:08:22Z

R/gkm.R

+#' @param bg_fill Optional color string for the plot background.
+#' @keywords internal
+#' @return A \code{ggplot2} object representing the table.
+#' @importFrom ggplot2 ggplot theme_void scale_x_continuous scale_y_continuous theme element_rect annotate element_text .pt


we have the import. Is enought to add the @import for the package

Melkiades · 2025-12-01T14:09:25Z

R/crane-package.R

 #' @keywords internal
 #' @import rlang
 #' @import glue glue
+#' @importFrom utils tail


I would import ggplot2 here

Melkiades · 2025-12-01T14:10:35Z

R/gkm.R

+f_conf_level <- function(conf_level) {
+  # assert_proportion_value(conf_level) # Assuming assert_proportion_value is defined elsewhere
+  paste0(conf_level * 100, "% CI")
+}
+
+control_surv_med_annot <- function(x = 0.8, y = 0.85, w = 0.32, h = 0.16, fill = TRUE) {
+  # assert_proportion_value(x)
+  # assert_proportion_value(y)
+  # assert_proportion_value(w)
+  # assert_proportion_value(h)
+
+  list(x = x, y = y, w = w, h = h, fill = fill)
+}
+
+control_coxph_annot <- function(x = 0.29, y = 0.51, w = 0.4, h = 0.125, fill = TRUE, ref_lbls = FALSE) {
+  checkmate::assert_logical(ref_lbls, any.missing = FALSE)
+
+  res <- c(control_surv_med_annot(x = x, y = y, w = w, h = h), list(ref_lbls = ref_lbls))
+  res
+}


maybe is best if all help functions are into an help file (utils_plot?)

Melkiades · 2025-12-01T14:11:37Z

R/gkm.R

+#' @importFrom broom tidy
+#' @importFrom tidyr pivot_wider
+#' @importFrom cowplot plot_grid
+#' @importFrom ggplot2 labs theme_bw theme element_text element_blank element_line coord_cartesian scale_x_continuous scale_y_continuous


should we keep the imports here?

Missing examples

init commit

70ec9a0

Merge branch 'main' into adding_g_km

105a6dc

shajoezhu added 8 commits November 28, 2025 23:39

update

6d8d156

Merge branch 'adding_g_km' of github.com:insightsengineering/crane in…

c3bbe60

…to adding_g_km

wip

41b7497

wordlist

9b8807a

adding code

6b51033

update ad test

2912448

update namespace

015b86e

update doc

ec08202

shajoezhu mentioned this pull request Nov 30, 2025

g_km refactoring #142

Open

3 tasks

shajoezhu added 12 commits December 1, 2025 09:43

rm code

585ee24

rm doc

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modify code

b29d65d

update

44b191c

updat epkgdown

770c10b

restyle:

9c2ef03

update

10e6312

update test

1512115

update doc

1e3fa5d

not using ggsurvfit yet

de896d3

restyle test

c65cf11

update assertion

4364b7a

shajoezhu added 4 commits December 1, 2025 19:35

update assertion

065ca7d

update test

889c21a

update

afebed3

update

8f52316

Melkiades reviewed Dec 1, 2025

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manual vbump

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