Resolving Merge Conflicts for #112 #115

ddsjoberg · 2024-04-15T00:18:50Z

@ayogasekaram recently updated function names to follow our convention ard_<pkg>_<fn>(), and @edelarua added cli environment handling. Both updates resulted in a large number of changes to files and file names.

This PR is going into @edelarua 's PR for adding the cli env handling (#112), and is meant to resolve all the conflicts. Can you both please review and approve this PR? Please check that I haven't undone any of your important changes from either initiative? Apologies for the incredibly poor planning on my part. 😬

@ayogasekaram

**What changes are proposed in this pull request?** Functions are renamed according to new conventions: `ard_<pkgname>_<fnname>()` if a package specific function is used If a `.` appears in a function name it will be replaced with a `_` in the ard_*() function name. closes #106 @ayogasekaram -------------------------------------------------------------------------------- Pre-review Checklist (if item does not apply, mark is as complete) - [x] **All** GitHub Action workflows pass with a ✅ - [x] PR branch has pulled the most recent updates from master branch: `usethis::pr_merge_main()` - [x] If a bug was fixed, a unit test was added. - [x] If a new `ard_*()` function was added, it passes the ARD structural checks from `cards::check_ard_structure()`. - [x] Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): `devtools::test_coverage()` - [x] Request a reviewer Reviewer Checklist (if item does not apply, mark is as complete) - [x] If a bug was fixed, a unit test was added. - [x] Run `pkgdown::build_site()`. Check the R console for errors, and review the rendered website. - [x] Code coverage is suitable for any new functions/features: `devtools::test_coverage()` When the branch is ready to be merged: - [x] 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". --------- Co-authored-by: Daniel Sjoberg <[email protected]>

**What changes are proposed in this pull request?** add `ard_aod_wald_test` function closes #84 -------------------------------------------------------------------------------- Pre-review Checklist (if item does not apply, mark is as complete) - [x] **All** GitHub Action workflows pass with a ✅ - [x] PR branch has pulled the most recent updates from master branch: `usethis::pr_merge_main()` - [x] If a bug was fixed, a unit test was added. - [x] If a new `ard_*()` function was added, it passes the ARD structural checks from `cards::check_ard_structure()`. - [x] Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): `devtools::test_coverage()` - [x] Request a reviewer Reviewer Checklist (if item does not apply, mark is as complete) - [x] If a bug was fixed, a unit test was added. - [x] Run `pkgdown::build_site()`. Check the R console for errors, and review the rendered website. - [x] Code coverage is suitable for any new functions/features: `devtools::test_coverage()` When the branch is ready to be merged: - [x] 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). - [x] **All** GitHub Action workflows pass with a ✅ - [x] Approve Pull Request - [x] Merge the PR. Please use "Squash and merge" or "Rebase and merge". --------- Signed-off-by: Daniel Sjoberg <[email protected]> Signed-off-by: Abinaya Yogasekaram <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]>

**What changes are proposed in this pull request?** - `ard_stats_anova()` for calculating ANOVA results using `stats::anova()`. (#12) There are two implementations of this function via S3 methods. 1. The first is when a user calculates the `anova()` object and passes it to `ard_stats_anova()`. 2. The second is when a user passes a data frame. We use that data frame and information from the other arguments to construct the models and pass the models to `anova()` **Reference GitHub issue associated with pull request.** _e.g., 'closes #<issue number>'_ closes #12 -------------------------------------------------------------------------------- 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()` - [ ] Request a reviewer Reviewer Checklist (if item does not apply, mark is as complete) - [x] If a bug was fixed, a unit test was added. - [x] Run `pkgdown::build_site()`. Check the R console for errors, and review the rendered website. - [x] 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". --------- Signed-off-by: Daniel Sjoberg <[email protected]> Co-authored-by: Emily de la Rua <[email protected]>

github-actions · 2024-04-15T00:27:39Z

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%   34-37, 49, 83
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      12  88.46%   118-124, 187-191
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_survfit.R          180       8  95.56%   78-80, 84, 94-96, 246
R/proportion_ci.R                 194      28  85.57%   290, 293, 302-307, 315, 330, 430-453
TOTAL                            1892      88  95.35%

Diff against main

Filename                        Stmts    Miss  Cover
----------------------------  -------  ------  --------
R/ard_aod_wald_test.R              +3      +2  -2.28%
R/ard_car_anova.R                  +4       0  +0.43%
R/ard_car_vif.R                    +3      +1  -1.22%
R/ard_effectsize_cohens_d.R        +1       0  +0.03%
R/ard_effectsize_hedges_g.R        +1       0  +0.03%
R/ard_proportion_ci.R              +2       0  +0.60%
R/ard_regression_basic.R           +1       0  +0.48%
R/ard_regression.R                 +1       0  +100.00%
R/ard_smd_smd.R                    +1       0  +0.03%
R/ard_stats_anova.R                +5      +3  -2.45%
R/ard_stats_aov.R                  +1       0  +100.00%
R/ard_stats_chisq_test.R           +1       0  +0.07%
R/ard_stats_fisher_test.R          +1       0  +0.06%
R/ard_stats_kruskal_test.R         +1       0  +0.08%
R/ard_stats_mcnemar_test.R         +1       0  +0.04%
R/ard_stats_mood_test.R            +1       0  +0.04%
R/ard_stats_oneway_test.R          +1       0  +100.00%
R/ard_stats_prop_test.R            +4       0  +0.06%
R/ard_stats_t_test.R              +14       0  +0.27%
R/ard_stats_wilcox_test.R          -8       0  -0.16%
R/ard_survey_svychisq.R            +1       0  +0.08%
R/ard_survey_svycontinuous.R       +1       0  +0.01%
R/ard_survey_svyranktest.R         +1       0  +100.00%
R/ard_survey_svyttest.R            +1       0  +100.00%
R/ard_survival_survfit.R           +7      +4  -2.13%
R/proportion_ci.R                  +6       0  +0.46%
TOTAL                             +56     +10  -0.40%

Results for commit: e04c13a

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2024-04-15T00:27:46Z

Unit Tests Summary

1 files ± 0 56 suites +3 8s ⏱️ -1s
56 tests + 4 37 ✅ + 4 19 💤 ±0 0 ❌ ±0
152 runs +11 117 ✅ +10 35 💤 +1 0 ❌ ±0

Results for commit e04c13a. ± Comparison against base commit 07b82c3.

♻️ This comment has been updated with latest results.

edelarua

I believe that covers everything on my end! Thanks Daniel!!

ayogasekaram

looks good on my end as well @ddsjoberg! Thank you :)

ddsjoberg · 2024-04-15T14:38:29Z

Thank you @edelarua @ayogasekaram for the review!!

ayogasekaram and others added 8 commits April 11, 2024 21:06

[skip actions] Bump version to 0.1.0.9012

8fa77ab

[skip actions] Bump version to 0.1.0.9013

452faa6

[skip actions] Bump version to 0.1.0.9014

c633acb

Merge commit 'c633acb06ba84db032154d29b84cd60b4112edb9'

237d012

resolving merge conflicts

b1ff0bf

ddsjoberg requested review from edelarua and ayogasekaram April 15, 2024 00:18

ddsjoberg changed the base branch from 42_cli_call_fun@main to main April 15, 2024 00:19

ddsjoberg changed the base branch from main to 42_cli_call_fun@main April 15, 2024 00:20

ddsjoberg added 2 commits April 14, 2024 17:21

Update check.yaml

1a7aeda

workflow updates

ee381e5

ddsjoberg added 5 commits April 14, 2024 17:28

styler

47a7eb0

Update NEWS.md

294e667

doc updates

83d3805

more updates

c9f7506

style

e04c13a

edelarua approved these changes Apr 15, 2024

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ayogasekaram approved these changes Apr 15, 2024

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ddsjoberg merged commit 39070ce into 42_cli_call_fun@main Apr 15, 2024
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ddsjoberg deleted the 42_merge-conflict-h-e-l-l branch April 15, 2024 14:38

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Resolving Merge Conflicts for #112 #115

Resolving Merge Conflicts for #112 #115

ddsjoberg commented Apr 15, 2024 •

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ddsjoberg commented Apr 15, 2024

Resolving Merge Conflicts for #112 #115

Resolving Merge Conflicts for #112 #115

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