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change cohort_id and strata to subject_var and group_var. #1106

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merged 12 commits into from
Nov 1, 2023

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ayogasekaram
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closes #1105
should the strata_N object in the function be renamed to group_N?

@Melkiades
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closes #1105 should the strata_N object in the function be renamed to group_N?

what do you think @clarkliming ?

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github-actions bot commented Oct 19, 2023

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Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      67       2  97.01%   76-77
R/abnormal_by_marked.R                        54       5  90.74%   115-119
R/abnormal_by_worst_grade_worsen.R           115       3  97.39%   233-235
R/abnormal_by_worst_grade.R                   39       0  100.00%
R/abnormal.R                                  42       0  100.00%
R/analyze_variables.R                        199       9  95.48%   476-477, 493, 696-697, 702-703, 721-722
R/analyze_vars_in_cols.R                     176      34  80.68%   167-168, 205-210, 225, 239-240, 248-256, 262-268, 347-353
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        124      17  86.29%   127-131, 243, 321-330, 384-385, 391
R/control_incidence_rate.R                    20       8  60.00%   32-35, 38-41
R/control_logistic.R                           7       0  100.00%
R/control_step.R                              23       1  95.65%   58
R/control_survival.R                          15       0  100.00%
R/count_cumulative.R                          49       1  97.96%   63
R/count_missed_doses.R                        33       0  100.00%
R/count_occurrences_by_grade.R               105       4  96.19%   156-158, 161
R/count_occurrences.R                        119       6  94.96%   92, 162-166
R/count_patients_events_in_cols.R             68       1  98.53%   62
R/count_patients_with_event.R                 46       0  100.00%
R/count_patients_with_flags.R                 57       4  92.98%   71-72, 77-78
R/count_values.R                              26       0  100.00%
R/cox_regression_inter.R                     154       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    167       7  95.81%   191-195, 239, 254, 262, 268-269
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            168      40  76.19%   232-263, 323-325, 331, 352-389
R/desctools_binom_diff.R                     621      64  89.69%   53, 88-89, 125-126, 129, 199, 223-232, 264, 266, 286, 290, 294, 298, 353, 356, 359, 362, 422, 430, 439, 444-447, 454, 457, 466, 469, 516-517, 519-520, 522-523, 525-526, 593, 604-616, 620, 663, 676, 680
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  49       1  97.96%   60
R/estimate_proportion.R                      201      12  94.03%   75-82, 86, 91, 298, 465, 570
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     174       3  98.28%   145, 155, 280
R/g_forest.R                                 438      21  95.21%   199, 319, 336-337, 342-343, 356, 372, 419, 450, 526, 535, 616-620, 630, 705, 708, 832
R/g_lineplot.R                               206      34  83.50%   166, 179, 208, 234-237, 313-320, 338-339, 345-355, 447, 453, 455, 497-498, 502-503
R/g_step.R                                    68       1  98.53%   109
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        73       0  100.00%
R/h_biomarkers_subgroups.R                    42       0  100.00%
R/h_cox_regression.R                         110       0  100.00%
R/h_logistic_regression.R                    468       3  99.36%   206-207, 276
R/h_map_for_count_abnormal.R                  57       2  96.49%   77-78
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           75       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   257-270
R/h_stack_by_baskets.R                        67       3  95.52%   68-69, 95
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           79       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   259-271
R/imputation_rule.R                           17       2  88.24%   54-55
R/incidence_rate.R                            95       7  92.63%   53-60
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        683      65  90.48%   230-233, 273-308, 317-321, 530, 717-719, 727-729, 761-762, 935-938, 1161, 1478-1489
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               108       0  100.00%
R/prop_diff_test.R                            90       0  100.00%
R/prop_diff.R                                262      16  93.89%   72-75, 107, 271-278, 417, 477, 582
R/prune_occurrences.R                         57      10  82.46%   138-142, 188-192
R/response_biomarkers_subgroups.R             60       0  100.00%
R/response_subgroups.R                       165       4  97.58%   268, 312-314
R/riskdiff.R                                  52       7  86.54%   88-91, 100, 110-111
R/rtables_access.R                            38       4  89.47%   159-162
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      59       3  94.92%   73-74, 129
R/summarize_ancova.R                          97       1  98.97%   180
R/summarize_change.R                          29       0  100.00%
R/summarize_colvars.R                         12       2  83.33%   72-73
R/summarize_coxreg.R                         174       6  96.55%   196-197, 204, 340-341, 434
R/summarize_glm_count.R                      166      29  82.53%   158, 162-213, 261-262
R/summarize_num_patients.R                   101       9  91.09%   105-107, 156-157, 240-245
R/summarize_patients_exposure_in_cols.R       98       1  98.98%   56
R/survival_biomarkers_subgroups.R             60       0  100.00%
R/survival_coxph_pairwise.R                   75       9  88.00%   59-67
R/survival_duration_subgroups.R              174       0  100.00%
R/survival_time.R                             49       0  100.00%
R/survival_timepoint.R                       120       7  94.17%   126-132
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       122       3  97.54%   482-485
R/utils_factor.R                             109       2  98.17%   84, 302
R/utils_grid.R                               111       5  95.50%   149, 258-264
R/utils_rtables.R                             90       7  92.22%   24, 31-35, 376-377
R/utils_split_funs.R                          52       2  96.15%   81, 93
R/utils.R                                    137      10  92.70%   92, 94, 98, 118, 121, 124, 128, 137-138, 311
TOTAL                                       9747     525  94.61%

Diff against main

Filename          Stmts    Miss  Cover
--------------  -------  ------  -------
R/g_lineplot.R       +6      +4  -1.50%
TOTAL                +6      +4  -0.04%

Results for commit: 16271a3

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Oct 19, 2023

Unit Tests Summary

       1 files       81 suites   1m 12s ⏱️
   794 tests    774 ✔️   20 💤 0
1 687 runs  1 049 ✔️ 638 💤 0

Results for commit 16271a3.

♻️ This comment has been updated with latest results.

@BFalquet
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closes #1105 should the strata_N object in the function be renamed to group_N?

what do you think @clarkliming ?

We will probably shield it so it doesn't really matter for now but maybe on the long(er) run

@shajoezhu
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i am inclined to block this pr, and merge it in the next PI, potential breaking change @Melkiades @ayogasekaram @edelarua @BFalquet @clarkliming , let me know what you think

@BFalquet
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i am inclined to block this pr, and merge it in the next PI, potential breaking change @Melkiades @ayogasekaram @edelarua @BFalquet @clarkliming , let me know what you think

We are wrapping it so no problem on our side, we can postpone.

@Melkiades
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@ayogasekaram can you open PRs in scda.test and TLG-c to accommodate these changes?

@ayogasekaram
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@Melkiades I've put up a PR in tlg-c which can be merged after the description file is updated. scda.test does not cover graphs currently so there is nothing to update there. I will create a separate issue to include plots in scda.test and add this to the task list.

@@ -5,12 +5,14 @@
#' Line plot with the optional table.
#'
#' @param df (`data.frame`)\cr data set containing all analysis variables.
#' @param alt_counts_df (`data.frame` or `NULL`)\cr data set that will be used (only) to counts objects in strata.
#' @param alt_counts_df (`data.frame` or `NULL`)\cr data set that will be used (only)
#' to counts objects in groups for stratification.
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Can you still add (or strata) after group where you specified it? so we get a bit of continuity and its searchable

#' @param variables (named `character` vector) of variable names in `df` data set. Details are:
#' * `x` (`character`)\cr name of x-axis variable.
#' * `y` (`character`)\cr name of y-axis variable.
#' * `strata` (`character`)\cr name of grouping variable, i.e. treatment arm. Can be `NA` to indicate lack of groups.
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we need to deprecate it I think (the same goes for the other param changes). Follow what Emily did with na_level :)

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Lgtm! Thanks Abi :)

@ayogasekaram ayogasekaram merged commit 9af3b5c into main Nov 1, 2023
24 checks passed
@ayogasekaram ayogasekaram deleted the 1105_fix_params@main branch November 1, 2023 14:31
ayogasekaram added a commit to insightsengineering/tlg-catalog that referenced this pull request Nov 1, 2023
closes #136 

merge after:

- [x] merging [this
PR](insightsengineering/tern#1106) in tern
- [x] Update tern package version in DESCRIPTION
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argument name is misleading for g_lineplot
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