Replace table by plot on tm_missing_data

[llrs-roche]

Pull Request

Fixes #495

Replaces the table by a plot on "By Variables Levels" tab.
The colors match those in the other plots of the module.
It also required to add a "new" dependency, formatters, which is a dependency of tern, rlistings, rtable. I added it on Suggests.

There is an extra commit to update the lintr names

data <- within(teal_data(), {
  ADSL <- rADSL
  ADRS <- rADRS
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

init(
  data = data,
  modules = modules(tm_missing_data())
) |> runApp()

[github-actions]

Code Coverage Summary

Filename                      Stmts    Miss  Cover    Missing
--------------------------  -------  ------  -------  -------------------------------------------
R/tm_a_pca.R                    865     865  0.00%    141-1133
R/tm_a_regression.R             751     751  0.00%    180-1027
R/tm_data_table.R               200     200  0.00%    100-348
R/tm_file_viewer.R              172     172  0.00%    47-254
R/tm_front_page.R               143     132  7.69%    77-246
R/tm_g_association.R            320     320  0.00%    161-547
R/tm_g_bivariate.R              670     406  39.40%   332-786, 827, 938, 955, 973, 984-1006
R/tm_g_distribution.R          1106    1106  0.00%    156-1404
R/tm_g_response.R               345     345  0.00%    179-594
R/tm_g_scatterplot.R            709     709  0.00%    261-1065
R/tm_g_scatterplotmatrix.R      272     253  6.99%    200-501, 562, 576
R/tm_missing_data.R            1183    1183  0.00%    126-1487
R/tm_outliers.R                1027    1027  0.00%    162-1339
R/tm_t_crosstable.R             263     263  0.00%    177-482
R/tm_variable_browser.R         788     783  0.63%    89-1025, 1063-1246
R/utils.R                       185     120  35.14%   87-249, 278-304, 316-325, 330, 344-363, 452
R/zzz.R                           2       2  0.00%    2-3
TOTAL                          9001    8637  4.04%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  --------
R/tm_missing_data.R     +103    +103  +100.00%
R/tm_outliers.R           +1      +1  +100.00%
TOTAL                   +104    +104  -0.05%

Results for commit: 8a311f1

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   23 suites   25m 18s ⏱️
151 tests 136 ✅ 5 💤 2 ❌ 8 🔥
453 runs  434 ✅ 5 💤 6 ❌ 8 🔥

For more details on these failures and errors, see this check.

Results for commit 8a311f1.

♻️ This comment has been updated with latest results.

[llrs-roche]

Branch code removed and some other code removal.
Linters with nolint start/end end with a dot.

See also the reply on formatters, if arguments are not convincing I'll move it to Imports.

[Copilot]

Pull Request Overview

This PR replaces the “By Variable Levels” table in tm_missing_data with a plot, updates the module’s outputs/decorators accordingly, and standardizes library loading strings across modules. It also adds the formatters package to Suggests.

• Replace “By Variable Levels” table with a new ggplot output (by_variable_plot) and wire it into UI, server, decorators, and reporter dims.
• Update documentation to list by_variable_plot and its decorator, and standardize eval_code library strings.
• Add formatters (>= 0.5.11) to Suggests.

Reviewed Changes

Copilot reviewed 15 out of 15 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
R/tm_missing_data.R	Switch “By Variable Levels” from a DT table to a ggplot, add decorator plumbing, and integrate plot_with_settings.
man/tm_missing_data.Rd	Document the new by_variable_plot output and decorator usage.
DESCRIPTION	Add formatters (>= 0.5.11) to Suggests.
R/tm_outliers.R, R/tm_t_crosstable.R, R/tm_g_scatterplotmatrix.R, R/tm_g_scatterplot.R, R/tm_g_response.R, R/tm_g_distribution.R, R/tm_g_bivariate.R, R/tm_g_association.R, R/tm_data_table.R, R/tm_a_regression.R, R/tm_a_pca.R	Standardize library loading strings in eval_code and adjust nolint comments.
R/teal.modules.general.R	Adjust nolint block markers.

---

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[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
shinytest2-tm_a_pca	💔	$156.94$	$+2.70$	$0$	$0$	$0$	$0$
shinytest2-tm_a_regression	💔	$71.23$	$+1.89$	$0$	$0$	$0$	$0$
shinytest2-tm_g_bivariate	💔	$91.22$	$+1.40$	$0$	$0$	$0$	$0$
shinytest2-tm_g_scatterplot	💔	$86.38$	$+2.38$	$0$	$0$	$0$	$0$
shinytest2-tm_missing_data	👶		$+47.34$	$+19$	$0$	$+6$	$+2$
shinytest2-tm_misssing_data	💀	$63.29$	$-63.29$	$-22$	$0$	$0$	$0$
shinytest2-tm_outliers	💔	$150.16$	$+3.03$	$0$	$0$	$0$	$0$
shinytest2-tm_variable_browser	💔	$78.30$	$+542.56$	$-17$	$0$	$0$	$+6$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
shinytest2-tm_missing_data	👶		$+12.33$	e2e_tm_missing_data_Check_default_settings_and_visibility_of_the_combinations_graph_and_encodings
shinytest2-tm_missing_data	👶		$+13.36$	e2e_tm_missing_data_Default_settings_and_visibility_of_the_summary_graph
shinytest2-tm_missing_data	👶		$+6.59$	e2e_tm_missing_data_Initializes_without_errors
shinytest2-tm_missing_data	👶		$+7.45$	e2e_tm_missing_data_Validate_By_Variable_Levels_table_values
shinytest2-tm_missing_data	👶		$+7.61$	e2e_tm_missing_data_Validate_functionality_and_UI_response_for_By_Variable_Levels_
shinytest2-tm_misssing_data	💀	$15.59$	$-15.59$	e2e_tm_missing_data_Check_default_settings_and_visibility_of_the_combinations_graph_and_encodings
shinytest2-tm_misssing_data	💀	$16.56$	$-16.56$	e2e_tm_missing_data_Default_settings_and_visibility_of_the_summary_graph
shinytest2-tm_misssing_data	💀	$7.76$	$-7.76$	e2e_tm_missing_data_Initializes_without_errors
shinytest2-tm_misssing_data	💀	$9.62$	$-9.62$	e2e_tm_missing_data_Validate_By_Variable_Levels_table_values
shinytest2-tm_misssing_data	💀	$13.77$	$-13.77$	e2e_tm_missing_data_Validate_functionality_and_UI_response_for_By_Variable_Levels_
shinytest2-tm_variable_browser	💔	$12.01$	$+91.48$	e2e_tm_variable_browser_Selecting_treat_variable_as_factor_changes_the_table_headers.
shinytest2-tm_variable_browser	💔	$13.58$	$+89.89$	e2e_tm_variable_browser_changing_display_density_encoding_doesn_t_show_errors.
shinytest2-tm_variable_browser	💔	$15.46$	$+88.00$	e2e_tm_variable_browser_changing_outlier_definition_encoding_doesn_t_show_errors.
shinytest2-tm_variable_browser	💔	$16.63$	$+86.85$	e2e_tm_variable_browser_changing_plot_setting_encodings_doesn_t_show_errors.
shinytest2-tm_variable_browser	💔	$10.63$	$+92.88$	e2e_tm_variable_browser_content_is_displayed_correctly.
shinytest2-tm_variable_browser	💔	$10.00$	$+93.46$	e2e_tm_variable_browser_selection_of_categorical_variable_has_a_table_with_level_header.

Results for commit aa67b0e

♻️ This comment has been updated with latest results.

[m7pr]

Hey @llrs-roche I saw 2 tests are failing

[m7pr]

@llrs-roche I see still issues with R CMD CHECK