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Adding model construction helpers #121

Merged
merged 11 commits into from
Apr 19, 2024
Merged

Adding model construction helpers #121

merged 11 commits into from
Apr 19, 2024

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ddsjoberg
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@ddsjoberg ddsjoberg commented Apr 16, 2024 •
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What changes are proposed in this pull request?

  • Adding functions to assist in constructing models construct_model(), reformulate2() (similar to stats::reformulate() but adds backticks around variable names with spaces in them), bt() (adds backtics to variable as needed), and bt_strip() (removes backticks from character variable names).

I also updated ard_survey_svychisq() to use reformulate2() instead of stats::reformulate() which allows variable names with spaces in them. Other instances of stats::reformulate() should also be updated in the future.

The reason we're adding the constructors is because the full ARS (Analysis Result Standard) requires that we begin with a data frame, and these help us take a data frame, a response variable, and covariates to construct complex models.

Reference GitHub issue associated with pull request. e.g., 'closes #'
closes #108

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()

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 16, 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                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          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/construction_helpers.R           42       6  85.71%   113, 125-129
R/proportion_ci.R                 194      28  85.57%   290, 293, 302-307, 315, 330, 431-454
TOTAL                            2014      82  95.93%

Diff against main

Filename                    Stmts    Miss  Cover
------------------------  -------  ------  -------
R/ard_stats_anova.R            -9      -5  +4.81%
R/construction_helpers.R      +42      +6  +85.71%
TOTAL                         +33      +1  +0.02%

Results for commit: 531d054

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Apr 16, 2024 •
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Unit Tests Summary

  1 files   60 suites   8s ⏱️
 60 tests  40 ✅ 20 💤 0 ❌
164 runs  128 ✅ 36 💤 0 ❌

Results for commit 531d054.

♻️ This comment has been updated with latest results.

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github-actions bot commented Apr 16, 2024 •
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Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
construction_helpers 👶 $+0.29$ $+1$ $+1$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
construction_helpers 👶 $+0.29$ construct_model_works

Results for commit 37139ef

♻️ This comment has been updated with latest results.

@ddsjoberg ddsjoberg mentioned this pull request Apr 16, 2024
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ddsjoberg commented Apr 16, 2024 •
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@shajoezhu @edelarua @ayogasekaram @Melkiades @zdz2101 I've added a function called reformulate2() in this PR. It is a simple wrapper for stats::reformulate() but will add backticks to your variable if is has a space in the variable name (the original function errors in this case).

Are there other characters that would require backticks to work properly?

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@shajoezhu @edelarua @ayogasekaram @Melkiades @zdz2101 I've added a function called reformulate2() in this PR. It is a simple wrapper for stats::reformulate() but will add backticks to your variable if is has a space in the variable name (the original function errors in this case).

Are there other characters that would require backticks to work properly?

The only other things I saw as special characters are \n and \r (but the latter was likely a typo, considering what it does, ahah). I suspect it would work nonetheless

@ddsjoberg
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Thanks @Melkiades ! I updated the default regex match to be bt(x, pattern = "[ \n\r]")

ayogasekaram
ayogasekaram approved these changes Apr 19, 2024
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looks great! Thanks @ddsjoberg

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thank you @ayogasekaram !!

@ddsjoberg ddsjoberg merged commit 0c5fd0b into main Apr 19, 2024
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@ddsjoberg ddsjoberg deleted the 108-construct_model branch April 19, 2024 17:02
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@ayogasekaram ayogasekaram ayogasekaram approved these changes

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Separate function to construct models?
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@ddsjoberg @Melkiades @ayogasekaram