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Adding ard_survival_survdiff() #119

Merged
merged 11 commits into from
Apr 16, 2024
Merged

Adding ard_survival_survdiff() #119

merged 11 commits into from
Apr 16, 2024

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ddsjoberg
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@ddsjoberg ddsjoberg commented Apr 15, 2024

What changes are proposed in this pull request?

  • Adding ard_survival_survdiff() for creating results from survival::survdiff(). (Log-rank Test #113)

Reference GitHub issue associated with pull request. e.g., 'closes #'
closes #113


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.
  • If a new ard_*() function was added, it passes the ARD structural checks from cards::check_ard_structure().
  • Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): devtools::test_coverage()
  • If a new ard_*() function was added, set_cli_abort_call() has been set.
  • If a new ard_*() function was added and it depends on another package (such as, broom), is_pkg_installed("broom", reference_pkg = "cardx") has been set in the function call and the following added to the roxygen comments: @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom"", reference_pkg = "cardx"))

Reviewer Checklist (if item does not apply, mark is as complete)

  • If a bug was fixed, a unit test was added.
  • 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 "# cardx (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".

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github-actions bot commented Apr 15, 2024

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Code Coverage Summary

Filename                        Stmts    Miss  Cover    Missing
----------------------------  -------  ------  -------  ------------------------------------
R/ard_aod_wald_test.R              77       8  89.61%   36-41, 91, 94
R/ard_car_anova.R                  45       2  95.56%   62, 65
R/ard_car_vif.R                    61       6  90.16%   37-40, 52, 86
R/ard_effectsize_cohens_d.R        88       2  97.73%   66, 111
R/ard_effectsize_hedges_g.R        82       2  97.56%   65, 115
R/ard_proportion_ci.R              42       5  88.10%   68-72
R/ard_regression_basic.R           15       1  93.33%   46
R/ard_regression.R                 50       0  100.00%
R/ard_smd_smd.R                    55       1  98.18%   48
R/ard_stats_anova.R               104       5  95.19%   189-193
R/ard_stats_aov.R                  36       0  100.00%
R/ard_stats_chisq_test.R           39       1  97.44%   39
R/ard_stats_fisher_test.R          41       1  97.56%   39
R/ard_stats_kruskal_test.R         35       1  97.14%   38
R/ard_stats_mcnemar_test.R         49       1  97.96%   43
R/ard_stats_mood_test.R            48       1  97.92%   46
R/ard_stats_oneway_test.R          31       0  100.00%
R/ard_stats_prop_test.R            82       1  98.78%   40
R/ard_stats_t_test.R              110       2  98.18%   62, 108
R/ard_stats_wilcox_test.R          97       2  97.94%   62, 114
R/ard_survey_svychisq.R            37       1  97.30%   44
R/ard_survey_svycontinuous.R      193       2  98.96%   169, 179
R/ard_survey_svyranktest.R         51       0  100.00%
R/ard_survey_svyttest.R            50       0  100.00%
R/ard_survival_survdiff.R          89       0  100.00%
R/ard_survival_survfit.R          180       8  95.56%   79-81, 85, 95-97, 247
R/proportion_ci.R                 194      28  85.57%   290, 293, 302-307, 315, 330, 431-454
TOTAL                            1981      81  95.91%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/ard_stats_anova.R              0      -7  +6.73%
R/ard_survival_survdiff.R      +89       0  +100.00%
TOTAL                          +89      -7  +0.56%

Results for commit: 9bb9fb8

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Apr 15, 2024

Unit Tests Summary

  1 files   59 suites   8s ⏱️
 59 tests  40 ✅ 19 💤 0 ❌
163 runs  128 ✅ 35 💤 0 ❌

Results for commit 9bb9fb8.

♻️ This comment has been updated with latest results.

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github-actions bot commented Apr 15, 2024

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
ard_survival_survdiff 👶 $+0.00$ $+4$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
ard_stats_anova 👶 $+0.00$ ard_stats_anova.data.frame_error_messaging
ard_survival_survdiff 👶 $+0.00$ ard_survival_survdiff_error_messaging
ard_survival_survdiff 👶 $+0.23$ ard_survival_survdiff_works

Results for commit 6ff5e02

♻️ This comment has been updated with latest results.

@edelarua edelarua self-requested a review April 16, 2024 23:14
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This is great!! Thanks @ddsjoberg :)

@edelarua edelarua merged commit 5c5e25f into main Apr 16, 2024
28 checks passed
@edelarua edelarua deleted the 113-survival_survdiff branch April 16, 2024 23:34
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Log-rank Test
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