kmg plot #141

shajoezhu · 2025-11-28T05:48:03Z

What changes are proposed in this pull request?

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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 72 suites 1m 33s ⏱️
72 tests 72 ✅ 0 💤 0 ❌
183 runs 183 ✅ 0 💤 0 ❌

Results for commit 899f0b9.

♻️ 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	👶		$+0.02$	$+3$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
add_blank_rows	💔	$6.23$	$+1.05$	add_blank_rows_works
gg_km	👶		$+0.02$	df2gg_works_with_proper_x_axis_and_without
gg_km	👶		$+0.10$	gg_km_works_with_default_inputs

Results for commit 61160ab

♻️ 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                   50      13  74.00%   68-71, 74-77, 82, 92-95
R/gg_km_utils.R                          102      16  84.31%   94, 134-151, 167
R/gg_km.R                                143      37  74.13%   54-57, 74, 101, 175-180, 183-186, 196-198, 203-204, 238-240, 247-250, 254, 265-269, 282, 284-286
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                                   1903      89  95.32%

Diff against main

Filename                   Stmts    Miss  Cover
-----------------------  -------  ------  -------
R/annotate_gg_km.R          +137      +9  +93.43%
R/get_cox_pairwise_df.R      +50     +13  +74.00%
R/gg_km_utils.R             +102     +16  +84.31%
R/gg_km.R                   +143     +37  +74.13%
TOTAL                       +432     +75  -3.73%

Results for commit: 899f0b9

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

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

R/annotate_gg_km.R

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!

Melkiades · 2025-12-16T16:23:47Z

@shajoezhu do you know what is this?

✖ Failed to download gt 1.1.0 (aarch64-apple-darwin20)
✖ Failed to download xfun 0.54 (aarch64-apple-darwin20)

shajoezhu · 2025-12-16T17:24:22Z

@shajoezhu do you know what is this?

✖ Failed to download gt 1.1.0 (aarch64-apple-darwin20) ✖ Failed to download xfun 0.54 (aarch64-apple-darwin20)

@Melkiades , where did you see these?

R/gg_km_utils.R

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

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

R/annotate_gg_km.R Show resolved Hide resolved

remove tibble

1afde94

Melkiades added 2 commits December 11, 2025 16:04

fix docs

cde1575

change name

1c66e79

Melkiades added 2 commits December 16, 2025 17:01

fixes

74c794f

small check

2282e02

fix docs

e5768e0

Melkiades reviewed Dec 17, 2025

View reviewed changes

R/gg_km_utils.R Show resolved Hide resolved

adding column name

35c423f

shajoezhu enabled auto-merge (squash) December 18, 2025 03:26

fix style

899f0b9

shajoezhu merged commit 81fda25 into main Dec 18, 2025
34 checks passed

shajoezhu deleted the adding_g_km branch December 18, 2025 03:39

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kmg plot #141

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