Update ard_survival_survfit

[edelarua]

What changes are proposed in this pull request?

• Updated ard_survival_survfit to return std.error and n.risk statistics. (Updates for ard_survival_survfit() #139 )

@ddsjoberg as I currently have it, std.error gets transformed along with estimate, conf.low, and conf.high (with options "survival", "cumhaz", and "risk"), but if you think it's more informative to always return the untransformed std.error that can be updated.

Closes #139

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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.
• If a new ard_*() function was added, it passes the ARD structural checks from cards::check_ard_structure().
• 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"))
• Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): devtools::test_coverage()

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()

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• 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).
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[edelarua]

I have read the CLA Document and I hereby sign the CLA

[github-actions]

Unit Tests Summary

  1 files   64 suites   9s ⏱️
 64 tests  44 ✅ 20 💤 0 ❌
181 runs  149 ✅ 32 💤 0 ❌

Results for commit 1564b51.

[github-actions]

Code Coverage Summary

Filename                               Stmts    Miss  Cover    Missing
-----------------------------------  -------  ------  -------  ------------------------------------
R/ard_aod_wald_test.R                     77       8  89.61%   36-41, 91, 94
R/ard_attributes.survey.design.R           2       0  100.00%
R/ard_car_anova.R                         45       2  95.56%   62, 65
R/ard_car_vif.R                           61       2  96.72%   52, 86
R/ard_continuous.survey.design.R         194       2  98.97%   172, 182
R/ard_effectsize_cohens_d.R              102       2  98.04%   68, 121
R/ard_effectsize_hedges_g.R               97       2  97.94%   68, 127
R/ard_emmeans_mean_difference.R           70       0  100.00%
R/ard_proportion_ci.R                     42       5  88.10%   68-72
R/ard_regression_basic.R                  16       1  93.75%   46
R/ard_regression.R                        51       0  100.00%
R/ard_smd_smd.R                           68       5  92.65%   58, 84-87
R/ard_stats_anova.R                       95       0  100.00%
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                 42       1  97.62%   42
R/ard_stats_kruskal_test.R                35       1  97.14%   38
R/ard_stats_mcnemar_test.R                79       2  97.47%   63, 105
R/ard_stats_mood_test.R                   48       1  97.92%   46
R/ard_stats_oneway_test.R                 38       0  100.00%
R/ard_stats_prop_test.R                   84       1  98.81%   43
R/ard_stats_t_test_onesample.R            40       0  100.00%
R/ard_stats_t_test.R                     111       2  98.20%   65, 111
R/ard_stats_wilcox_test_onesample.R       41       0  100.00%
R/ard_stats_wilcox_test.R                 98       2  97.96%   65, 117
R/ard_survey_svychisq.R                   37       1  97.30%   44
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                 174      13  92.53%   79-81, 85, 95-97, 128-132, 237
R/construction_helpers.R                  60       6  90.00%   148, 160-164
R/proportion_ci.R                        194      28  85.57%   290, 293, 302-307, 315, 330, 431-454
TOTAL                                   2266      88  96.12%

Diff against main

Filename                    Stmts    Miss  Cover
------------------------  -------  ------  -------
R/ard_survival_survfit.R       -6      +5  -3.03%
TOTAL                          -6      +5  -0.23%

Results for commit: 6cb361d

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   67 suites   10s ⏱️
 67 tests  46 ✅ 21 💤 0 ❌
192 runs  159 ✅ 33 💤 0 ❌

Results for commit 6cb361d.

♻️ This comment has been updated with latest results.

[ddsjoberg]

Thank you @edelarua !!

@ddsjoberg as I currently have it, std.error gets transformed along with estimate, conf.low, and conf.high (with options "survival", "cumhaz", and "risk"), but if you think it's more informative to always return the untransformed std.error that can be updated.

When we perform a non-linear transformation on a standard error, standard deviation, or variance, we need to be very careful we perform the transformation appropriately (i.e. you could to use the delta method which requires the derivative of the transforming function). Let's keep it simple and not transform the std error, and we'll make it clear with the stat_label that this is the std error of the untransformed quantity. How does that sound?

[edelarua]

When we perform a non-linear transformation on a standard error, standard deviation, or variance, we need to be very careful we perform the transformation appropriately (i.e. you could to use the delta method which requires the derivative of the transforming function). Let's keep it simple and not transform the std error, and we'll make it clear with the stat_label that this is the std error of the untransformed quantity. How does that sound?

Sounds good @ddsjoberg! I have removed standard error from the transformed variables and changed its label to Standard Error (untransformed).

[edelarua]

@ddsjoberg this is ready for review when you have the time!!

[ddsjoberg]

Thank you @edelarua !!! this is great