kmg plot #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. (#, @)

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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 71 suites 1m 30s ⏱️
71 tests 71 ✅ 0 💤 0 ❌
179 runs 179 ✅ 0 💤 0 ❌

Results for commit 1c66e79.

♻️ 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`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
gg_km	👶		$+0.17$	$+3$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
gg_km	👶		$+0.17$	gg_km_works_with_default_inputs
tbl_shift	💚	$20.42$	$-1.16$	tbl_shift_strata_location_

Results for commit 75185b2

♻️ 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_difference_row.R                   101       0  100.00%
R/add_hierarchical_count_row.R            33       0  100.00%
R/annotate_gg_km.R                       137       9  93.43%   86-89, 108-112
R/crane-package.R                          2       2  0.00%    25-26
R/deprecated.R                             6       6  0.00%    15-21
R/get_cox_pairwise_df.R                   45      13  71.11%   68-71, 74-77, 82, 92-95
R/gg_km_utils.R                          100      17  83.00%   31, 87, 113-130, 146
R/gg_km.R                                142      37  73.94%   54-57, 74, 101, 178-183, 186-189, 198-200, 205-206, 240-242, 249-252, 256, 267-271, 284, 286-288
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                                   1895      90  95.25%

Diff against main

Filename                   Stmts    Miss  Cover
-----------------------  -------  ------  -------
R/annotate_gg_km.R          +137      +9  +93.43%
R/get_cox_pairwise_df.R      +45     +13  +71.11%
R/gg_km_utils.R             +100     +17  +83.00%
R/gg_km.R                   +142     +37  +73.94%
TOTAL                       +424     +76  -3.80%

Results for commit: 1c66e79

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’

shajoezhu · 2025-12-06T10:11:26Z

hi davide, can you fix the test please https://github.com/insightsengineering/crane/actions/runs/19936180249/job/57161536238 thanks

Signed-off-by: Davide Garolini <[email protected]>

…to adding_g_km

Melkiades

There is an issue with alignment that I still need to work on. It was already an issue in the first version of the template ;)

shajoezhu · 2025-12-09T20:36:03Z

There is an issue with alignment that I still need to work on. It was already an issue in the first version of the template ;)

for the risk table? I think that is minor, we can either create an issue to fix this, or move to ggsurft in the refacorting

shajoezhu · 2025-12-10T03:48:18Z

hi @Melkiades , thanks for the changes, i think it looks great!

Melkiades

I think it is good to go. There are other updates to be done but minor changes

Melkiades · 2025-12-11T14:47:26Z

R/annotate_gg_km.R

+  gg_coxph <- suppressMessages(
+    gg_coxph +
+      ggplot2::scale_x_continuous(expand = c(0.025, 0)) +
+      ggplot2::scale_y_continuous(labels = rev(rownames(coxph_tbl)), breaks = seq_len(nrow(coxph_tbl)))


This may benefit a refactoring as happened for annotate_risk

Melkiades · 2025-12-11T14:48:37Z

@shajoezhu we could use add_* instead of annotate_*? might be clearer

shajoezhu · 2025-12-11T14:59:44Z

@shajoezhu we could use add_* instead of annotate_*? might be clearer

honestly, i have no strong opinion on this

Melkiades · 2025-12-11T15:07:42Z

@shajoezhu we could use add_* instead of annotate_*? might be clearer

honestly, i have no strong opinion on this

probably not because it would create confusion with ggsurvfit (add_risktable function for example)

Melkiades · 2025-12-11T15:08:07Z

I think it is good to go @shajoezhu

shajoezhu · 2025-12-11T16:04:44Z

hi @Melkiades , can you fix the cicd thanks!

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

4c3268f

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

change name

452e26c

shajoezhu mentioned this pull request Dec 8, 2025

preparing for release 0.3.0, [skip vbump] #146

Draft

12 tasks

Melkiades and others added 3 commits December 8, 2025 17:20

finilizing

f7bdf13

fix

786f40b

Merge branch 'main' into adding_g_km

36ef6b4

Signed-off-by: Davide Garolini <[email protected]>

Melkiades marked this pull request as ready for review December 8, 2025 16:33

Melkiades added 6 commits December 8, 2025 17:35

fix

3b3b991

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

64d452a

…to adding_g_km

fix

0de370e

fix

1448707

final fix

98a5948

final fix 2

b4716e2

Melkiades requested changes Dec 9, 2025

View reviewed changes

shajoezhu requested a review from Melkiades December 10, 2025 03:47

Melkiades added 3 commits December 10, 2025 11:32

almost fixed

b09966d

fix order of values

4a5a258

example

4c14a69

Melkiades approved these changes Dec 11, 2025

View reviewed changes

Melkiades reviewed Dec 11, 2025

View reviewed changes

remove tibble

1afde94

Melkiades added 2 commits December 11, 2025 16:04

fix docs

cde1575

change name

1c66e79

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