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)

• 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".

[github-actions]

Unit Tests Summary

  1 files   70 suites   1m 38s ⏱️
 70 tests  70 ✅ 0 💤 0 ❌
176 runs  176 ✅ 0 💤 0 ❌

Results for commit 4174f6a.

♻️ 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	💔	$1.07$	$+5.50$	add_blank_rows_works
add_difference_row	👶		$+0.00$	add_difference_row.tbl_survfit_times_error_messaging_works
add_difference_row	👶		$+3.85$	add_difference_row.tbl_survfit_times_works
add_hierarchical_count_row	💚	$4.84$	$-4.62$	add_hierarchical_count_row_works
tbl_hierarchical_rate_and_count	💔	$18.80$	$+1.58$	tbl_hierarchical_rate_and_count_works
tbl_hierarchical_rate_by_grade	💔	$6.04$	$+1.07$	tbl_hierarchical_rate_by_grade_works
tbl_shift	💔	$19.73$	$+2.04$	tbl_shift_strata_location_

Results for commit 3c94a0b

♻️ 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                     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                                   1471      14  99.05%

Diff against main

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

Results for commit: 4174f6a

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[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.

[edelarua]

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.

@ddsjoberg I'm not sure if the two should be mixed - this function currently calculates the difference for each "level" of the table, in this case for every timepoint, but hazard ratios are calculated at base level (independent of any timepoints), so the input type would be different for HR calculations (doesn't need to by a tbl_survfit_times table). A separate function (or method) could be added for other tests/difference calculations. What do you think?

[ddsjoberg]

@ddsjoberg I'm not sure if the two should be mixed - this function currently calculates the difference for each "level" of the table, in this case for every timepoint, but hazard ratios are calculated at base level (independent of any timepoints), so the input type would be different for HR calculations (doesn't need to by a tbl_survfit_times table). A separate function (or method) could be added for other tests/difference calculations. What do you think?

This comment is more about keeping the function customizable/more generalizable with the test argument, which mirrors the functionality in the primary method. But it's your pkg now, do as you please!