Add add_difference_row.tbl_survfit_times for survival difference rows

[edelarua]

What changes are proposed in this pull request?

• Added function add_difference_row.tbl_survfit_times to add survival difference rows to survival time summary tables. (Add function to add difference statistics to tbl_survfit_times() tables #131)

Also:

• Updated default statistic formats for tbl_survfit_times() to align with catalog standard.
• Implemented skip_if_pkg_not_installed() in tests.

Closes #131

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Pre-review Checklist (if item does not apply, mark is as complete)

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• 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).
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• Approve Pull Request
• Merge the PR. Please use "Squash and merge" or "Rebase and merge".

[github-actions]

Unit Tests Summary

  1 files   69 suites   1m 32s ⏱️
 69 tests  69 ✅ 0 💤 0 ❌
174 runs  174 ✅ 0 💤 0 ❌

Results for commit a614153.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
add_difference_row	👶		$+0.00$	$+2$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
add_blank_rows	💔	$1.18$	$+5.39$	add_blank_rows_works
add_difference_row	👶		$+0.00$	add_difference_row.tbl_survfit_times_error_messaging_works
add_difference_row	👶		$+3.66$	add_difference_row.tbl_survfit_times_works
add_hierarchical_count_row	💚	$5.00$	$-4.53$	add_hierarchical_count_row_works
tbl_shift	💔	$20.20$	$+1.20$	tbl_shift_strata_location_

Results for commit c87b773

♻️ This comment has been updated with latest results.

[github-actions]

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/crane-package.R                          2       2  0.00%    17-18
R/deprecated.R                             6       6  0.00%    15-21
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                     184       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                     60       0  100.00%
R/tbl_shift.R                            115       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                                  5       0  100.00%
TOTAL                                   1433      14  99.02%

Diff against main

Filename                  Stmts    Miss  Cover
----------------------  -------  ------  --------
R/add_difference_row.R     +101       0  +100.00%
TOTAL                      +101       0  +0.07%

Results for commit: a614153

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[edelarua]

Should this be "Difference in Event Free Rate"? The GDSR has it with "Rates" but TLG catalog and STREAM with "Rate".

[ddsjoberg]

Thank you for putting this together!

I think we'll need to write it a bit more generally because while the survival differences are important to report, we'll also need to report items like hazards ratios, right? Let's meet to discuss our reporting needs.

[ddsjoberg]

This is great, thank you. At the moment this is hyper focussed to create the table from the spec. I wonder if there would be value in adding a test argument like the original add_difference_row() function so the users can change the difference statistics to, for example, hazard ratios. But this change would then require the catalog to add a call to modify_indent() to indent the last two rows further.