feat(picks): migrate tm_t_abnormality_by_worst_grade

[m7pr]

library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb %>%
    filter(!AVISIT %in% c("SCREENING", "BASELINE"))
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

app <- init(
  data = data,
  modules = modules(
    tm_t_abnormality_by_worst_grade(
      label = "Laboratory Test Results with Highest Grade Post-Baseline",
      dataname = "ADLB",
      arm_var = variables(choices = c("ARM", "ARMCD"), selected = "ARM"),
      paramcd = variables(choices = "PARAMCD"),
      add_total = FALSE
    )
  ),
  filter = teal_slices(
    teal_slice("ADSL", "SAFFL", selected = "Y"),
    teal_slice("ADLB", "ONTRTFL", selected = "Y")
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

[github-actions]

Unit Tests Summary

    1 files  ±0     70 suites  ±0   1h 33m 40s ⏱️ + 2m 18s
  713 tests +1    712 ✅ +1  1 💤 ±0  0 ❌ ±0 
1 731 runs  ±0  1 728 ✅ ±0  3 💤 ±0  0 ❌ ±0 

Results for commit 7d45124. ± Comparison against base commit 2423443.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test suite performance difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
shinytest2-tm_a_gee	💔	$0.25$	$+3.49$	$0$	$0$	$0$	$0$
shinytest2-tm_a_mmrm	💀	$0.69$	$-0.69$	$-48$	$-48$	$0$	$0$
shinytest2-tm_g_barchart_simple	💔	$0.34$	$+2.84$	$+2$	$+2$	$0$	$0$
shinytest2-tm_g_ci	💔	$0.21$	$+1.19$	$0$	$0$	$0$	$0$
shinytest2-tm_g_forest_rsp	💔	$0.26$	$+2.82$	$0$	$0$	$0$	$0$
shinytest2-tm_g_ipp	💔	$0.21$	$+2.93$	$0$	$0$	$0$	$0$
shinytest2-tm_g_km	💔	$0.41$	$+3.30$	$0$	$0$	$0$	$0$
shinytest2-tm_g_lineplot	💔	$0.16$	$+1.21$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_adverse_events	💔	$0.25$	$+1.96$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_patient_timeline	💔	$0.38$	$+4.93$	$0$	$0$	$0$	$0$
shinytest2-tm_g_pp_therapy	💚	$328.41$	$-320.46$	$-36$	$+23$	$0$	$0$
shinytest2-tm_t_abnormality	💔	$0.13$	$+1.17$	$0$	$0$	$0$	$0$
shinytest2-tm_t_abnormality_by_worst_grade	💔	$0.11$	$+1.03$	$0$	$0$	$0$	$0$
shinytest2-tm_t_ancova	💔	$0.18$	$+2.23$	$0$	$0$	$0$	$0$
shinytest2-tm_t_binary_outcome	💔	$0.15$	$+1.49$	$0$	$0$	$0$	$0$
shinytest2-tm_t_coxreg	💔	$0.16$	$+1.06$	$0$	$0$	$0$	$0$
shinytest2-tm_t_events_by_grade	💔	$0.14$	$+1.55$	$0$	$0$	$0$	$0$
shinytest2-tm_t_events_summary	💔	$0.11$	$+2.53$	$0$	$0$	$0$	$0$
shinytest2-tm_t_exposure	💔	$0.14$	$+3.01$	$0$	$0$	$0$	$0$
shinytest2-tm_t_pp_prior_medication	💔	$0.16$	$+1.61$	$0$	$0$	$0$	$0$
shinytest2-tm_t_shift_by_arm	💔	$0.11$	$+1.34$	$0$	$0$	$0$	$0$
shinytest2-tm_t_shift_by_arm_by_worst	💔	$0.16$	$+1.97$	$0$	$0$	$0$	$0$
shinytest2-tm_t_shift_by_grade	💔	$0.13$	$+1.92$	$0$	$0$	$0$	$0$
shinytest2-tm_t_smq	💔	$0.11$	$+1.33$	$0$	$0$	$0$	$0$
shinytest2-tm_t_summary_by	💔	$0.14$	$+1.56$	$0$	$0$	$0$	$0$
utils_picks	👶		$+0.37$	$+57$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
examples	👶		$+0.07$	example_arm_bucket_values.Rd
examples	👶		$+0.04$	example_arm_ref_comp_buckets_validator.Rd
examples	👶		$+0.01$	example_arm_ref_comp_observer_picks.Rd
examples	👶		$+0.01$	example_paramcd_title_from_anl.Rd
shinytest2-tm_a_gee	👶		$+0.04$	unnamed
shinytest2-tm_a_mmrm	💀	$0.02$	$-0.02$	e2e_tm_a_mmrm_Click_on_fit_model_shows_table_for_default_selection.
shinytest2-tm_a_mmrm	💀	$0.02$	$-0.02$	e2e_tm_a_mmrm_Deselection_of_arm_var_throws_validation_error_in_method_g_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_arm_var_throws_validation_error_in_method_g_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.02$	$-0.02$	e2e_tm_a_mmrm_Deselection_of_arm_var_throws_validation_error_in_method_t_mmrm_cov.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_arm_var_throws_validation_error_in_method_t_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_arm_var_throws_validation_error_in_method_t_mmrm_fixed.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_arm_var_throws_validation_error_in_method_t_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_aval_var_throws_validation_error_in_method_g_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_aval_var_throws_validation_error_in_method_g_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_aval_var_throws_validation_error_in_method_t_mmrm_cov.
shinytest2-tm_a_mmrm	💀	$0.02$	$-0.02$	e2e_tm_a_mmrm_Deselection_of_aval_var_throws_validation_error_in_method_t_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_aval_var_throws_validation_error_in_method_t_mmrm_fixed.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_aval_var_throws_validation_error_in_method_t_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_conf_level_throws_validation_error_in_method_g_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_conf_level_throws_validation_error_in_method_g_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_conf_level_throws_validation_error_in_method_t_mmrm_cov.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_conf_level_throws_validation_error_in_method_t_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_conf_level_throws_validation_error_in_method_t_mmrm_fixed.
shinytest2-tm_a_mmrm	💀	$0.02$	$-0.02$	e2e_tm_a_mmrm_Deselection_of_conf_level_throws_validation_error_in_method_t_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_id_var_throws_validation_error_in_method_g_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_id_var_throws_validation_error_in_method_g_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_id_var_throws_validation_error_in_method_t_mmrm_cov.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_id_var_throws_validation_error_in_method_t_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_id_var_throws_validation_error_in_method_t_mmrm_fixed.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_id_var_throws_validation_error_in_method_t_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_visit_var_throws_validation_error_in_method_g_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_visit_var_throws_validation_error_in_method_g_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_visit_var_throws_validation_error_in_method_t_mmrm_cov.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_visit_var_throws_validation_error_in_method_t_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_visit_var_throws_validation_error_in_method_t_mmrm_fixed.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_of_visit_var_throws_validation_error_in_method_t_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_paramcd_throws_validation_error_in_method_g_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_paramcd_throws_validation_error_in_method_g_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_paramcd_throws_validation_error_in_method_t_mmrm_cov.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_paramcd_throws_validation_error_in_method_t_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_paramcd_throws_validation_error_in_method_t_mmrm_fixed.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Deselection_paramcd_throws_validation_error_in_method_t_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Function_g_mmrm_diagnostic_selection_shows_output_settings_changing_settings_throws_no_validation_errors_and_verify_visibility_of_generated_plots.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Function_g_mmrm_lsmeans_selection_shows_output_settings_changing_settings_throws_no_validation_errors_and_verify_visibility_of_generated_plots.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Function_t_mmrm_lsmeans_selection_shows_output_settings_changing_settings_throws_no_validation_errors_and_verify_visibility_of_generated_tables.
shinytest2-tm_a_mmrm	💀	$0.02$	$-0.02$	e2e_tm_a_mmrm_Module_initializes_in_teal_without_errors_and_displays_a_message_to_click_Fit_Model_.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Module_initializes_with_specified_label_aval_var_paramcd_visit_var_cov_var_arm_var_buckets_combine_comp_arms_id_var_cor_struct_weights_emmeans_conf_level_method_parallel_and_output_function.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Validate_output_on_different_selection_on_method_g_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Validate_output_on_different_selection_on_method_g_mmrm_lsmeans.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Validate_output_on_different_selection_on_method_t_mmrm_cov.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Validate_output_on_different_selection_on_method_t_mmrm_diagnostic.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Validate_output_on_different_selection_on_method_t_mmrm_fixed.
shinytest2-tm_a_mmrm	💀	$0.01$	$-0.01$	e2e_tm_a_mmrm_Validate_output_on_different_selection_on_method_t_mmrm_lsmeans.
shinytest2-tm_g_pp_therapy	💚	$14.40$	$-14.09$	e2e_tm_g_pp_therapy_Changing_font_size_changes_the_plot_and_does_not_throw_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$13.52$	$-13.21$	e2e_tm_g_pp_therapy_Deselection_of_atirel_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$13.46$	$-13.15$	e2e_tm_g_pp_therapy_Deselection_of_cmdecod_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$13.38$	$-13.06$	e2e_tm_g_pp_therapy_Deselection_of_cmdose_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$13.60$	$-13.27$	e2e_tm_g_pp_therapy_Deselection_of_cmdosfrq_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$13.55$	$-13.00$	e2e_tm_g_pp_therapy_Deselection_of_cmdosu_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$14.32$	$-14.00$	e2e_tm_g_pp_therapy_Deselection_of_cmendy_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$13.35$	$-13.04$	e2e_tm_g_pp_therapy_Deselection_of_cmindc_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$13.50$	$-13.16$	e2e_tm_g_pp_therapy_Deselection_of_cmroute_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$13.26$	$-12.93$	e2e_tm_g_pp_therapy_Deselection_of_cmstdy_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$13.28$	$-12.96$	e2e_tm_g_pp_therapy_Deselection_of_patient_id_throws_validation_error.
shinytest2-tm_g_pp_therapy	💚	$18.35$	$-18.01$	e2e_tm_g_pp_therapy_Module_initializes_in_teal_without_errors_and_produces_output.
shinytest2-tm_g_pp_therapy	💚	$14.69$	$-14.36$	e2e_tm_g_pp_therapy_Selection_of_atirel_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$14.92$	$-14.59$	e2e_tm_g_pp_therapy_Selection_of_cmdecod_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$14.71$	$-14.37$	e2e_tm_g_pp_therapy_Selection_of_cmdose_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$14.50$	$-14.19$	e2e_tm_g_pp_therapy_Selection_of_cmdosfrq_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$14.82$	$-14.29$	e2e_tm_g_pp_therapy_Selection_of_cmdosu_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$14.91$	$-14.60$	e2e_tm_g_pp_therapy_Selection_of_cmendy_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$14.47$	$-14.12$	e2e_tm_g_pp_therapy_Selection_of_cmindc_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$14.74$	$-14.42$	e2e_tm_g_pp_therapy_Selection_of_cmroute_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$14.71$	$-14.39$	e2e_tm_g_pp_therapy_Selection_of_cmstdy_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$14.73$	$-14.40$	e2e_tm_g_pp_therapy_Selection_of_patient_id_changes_the_plot_and_table_without_any_validation_errors.
shinytest2-tm_g_pp_therapy	💚	$13.22$	$-12.85$	e2e_tm_g_pp_therapy_Starts_with_specified_label_paramcd_arm_var_buckets_paramcd_subgroup_var_strata_var_and_plot_settings.
utils_picks	👶		$+0.01$	create_picks_helper_errors_when_datasets_is_NULL
utils_picks	👶		$+0.01$	create_picks_helper_errors_when_datasets_is_not_a_datasets_object
utils_picks	👶		$+0.02$	create_picks_helper_errors_when_x_is_neither_pick_nor_picks
utils_picks	👶		$+0.01$	create_picks_helper_returns_x_unchanged_if_it_already_has_datasets_attached
utils_picks	👶		$+0.01$	create_picks_helper_wraps_a_pick_object_with_the_supplied_datasets
utils_picks	👶		$+0.01$	create_picks_helper_wraps_a_picks_object_without_datasets_with_the_supplied_datasets
utils_picks	👶		$+0.01$	migrate_choices_selected_to_values_errors_on_delayed_choices_selected
utils_picks	👶		$+0.01$	migrate_choices_selected_to_values_errors_when_input_is_not_a_picks_or_choices_selected_object
utils_picks	👶		$+0.01$	migrate_choices_selected_to_values_infers_multiple_TRUE_when_more_than_one_value_is_selected
utils_picks	👶		$+0.01$	migrate_choices_selected_to_values_preserves_fixed_TRUE_from_the_choices_selected_object
utils_picks	👶		$+0.01$	migrate_choices_selected_to_values_respects_the_multiple_argument
utils_picks	👶		$+0.02$	migrate_choices_selected_to_values_returns_a_teal.picks_values_object_from_a_choices_selected
utils_picks	👶		$+0.01$	migrate_choices_selected_to_values_returns_the_same_picks_object_if_input_already_inherits_picks
utils_picks	👶		$+0.01$	migrate_choices_selected_to_values_returns_variables_unchanged_column_pick_only_not_coerced_to_values_
utils_picks	👶		$+0.02$	migrate_choices_selected_to_variables_emits_a_deprecation_warning_for_choices_selected_input
utils_picks	👶		$+0.03$	migrate_choices_selected_to_variables_emits_a_deprecation_warning_for_select_spec_input
utils_picks	👶		$+0.01$	migrate_choices_selected_to_variables_errors_when_x_is_NULL_and_null.ok_FALSE
utils_picks	👶		$+0.01$	migrate_choices_selected_to_variables_returns_NULL_when_null.ok_TRUE_and_x_is_NULL
utils_picks	👶		$+0.01$	migrate_choices_selected_to_variables_returns_the_same_picks_object_if_input_already_inherits_picks
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_adds_values_when_ommited
utils_picks	👶		$+0.04$	migrate_value_choices_to_picks_returns_a_teal.picks_picks_object
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_returns_the_same_picks_object_if_input_is_already_a_picks_object
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_suports_picks_with_datasets_and_variables_but_no_values
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_suports_picks_with_datasets_and_variables_but_no_values_and_without_adding_values_
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_supports_only_variables_
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_supports_only_variables_without_adding_values
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_supports_picks_with_dataset_variables_and_values
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_supports_picks_with_only_variables
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_supports_picks_with_only_variables_and_does_not_add_values_
utils_picks	👶		$+0.01$	migrate_value_choices_to_picks_supports_picks_with_variables_and_values_but_no_datasets

Results for commit 448eeb6

♻️ This comment has been updated with latest results.

[osenan]

Great job! The only important issue is the module argument worst_flag_indicator. I think we should try to migrate to teal.values. There will be changes required in module, ui and server function. But if we do not change it, we will not complete the migration. This ui component is static, as it cannot be changed by the user. We could also just show the value by a simpler component that is not dynamic.

The other comments are minor and similar to what observed in tm_t_abnormality PR.

[m7pr]

@osenan I added some changes in here 9b7dd30

[osenan]

Good change including the argument worst_flag_indicator as values and the deprecation. However, the argument should be included in the ui as well and check that the example app is working as expected.
Once it is changed I review the e2e test and the funcionality of the module.
Once the helpers are ready include verifications on multiple attributes.
Please also fix the linters before merge.