Fix trailing "." when using format_sigfig, add functionality for multiple values

[edelarua]

Closes #1066

[github-actions]

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      63       0  100.00%
R/abnormal_by_marked.R                        53       5  90.57%   115-119
R/abnormal_by_worst_grade_worsen.R           114       3  97.37%   233-235
R/abnormal_by_worst_grade.R                   38       0  100.00%
R/abnormal.R                                  41       0  100.00%
R/analyze_variables.R                        192       5  97.40%   483, 686-687, 704-705
R/analyze_vars_in_cols.R                     166      29  82.53%   199-204, 219, 233-234, 242-247, 253-259, 334-340
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        120      15  87.50%   127-131, 243, 321-330, 385
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                          48       1  97.92%   63
R/count_missed_doses.R                        32       0  100.00%
R/count_occurrences_by_grade.R               103       4  96.12%   156-158, 161
R/count_occurrences.R                         73       1  98.63%   92
R/count_patients_events_in_cols.R             67       1  98.51%   62
R/count_patients_with_event.R                 45       0  100.00%
R/count_patients_with_flags.R                 56       4  92.86%   71-72, 77-78
R/count_values.R                              25       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                            169      40  76.33%   232-263, 323-325, 332, 353-390
R/desctools_binom_diff.R                     663      66  90.05%   52, 87-88, 128-129, 132, 211, 237-246, 285, 287, 307, 311, 315, 319, 375, 378, 381, 384, 445, 453, 465-466, 472-475, 483, 486, 495, 498, 546-547, 549-550, 552-553, 555-556, 626, 638-651, 656, 703, 716, 720
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  48       1  97.92%   60
R/estimate_proportion.R                      200      12  94.00%   75-82, 86, 91, 296, 463, 568
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     162       3  98.15%   145, 155, 243
R/g_forest.R                                 438      23  94.75%   199, 251-252, 319, 336-337, 342-343, 356, 372, 419, 450, 526, 535, 616-620, 630, 705, 708, 832
R/g_lineplot.R                               199      30  84.92%   160, 173, 201, 227-230, 307-314, 332-333, 339-349, 441, 447, 449
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                    40       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                  54       0  100.00%
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                        64       1  98.44%   89
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                            94       7  92.55%   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                      101       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               107       0  100.00%
R/prop_diff_test.R                            89       0  100.00%
R/prop_diff.R                                261      16  93.87%   72-75, 107, 269-276, 415, 475, 580
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                                  48       7  85.42%   85-88, 95, 105-106
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                          96       1  98.96%   180
R/summarize_change.R                          28       0  100.00%
R/summarize_colvars.R                          9       0  100.00%
R/summarize_coxreg.R                         165       2  98.79%   198, 420
R/summarize_glm_count.R                      165       5  96.97%   158, 162-163, 207, 260
R/summarize_num_patients.R                    97       9  90.72%   103-105, 153-154, 235-240
R/summarize_patients_exposure_in_cols.R       97       1  98.97%   56
R/survival_biomarkers_subgroups.R             60       0  100.00%
R/survival_coxph_pairwise.R                   74       9  87.84%   59-67
R/survival_duration_subgroups.R              172       0  100.00%
R/survival_time.R                             48       0  100.00%
R/survival_timepoint.R                       118       7  94.07%   126-132
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R        95       3  96.84%   408-411
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.R                                    137      10  92.70%   92, 94, 98, 118, 121, 124, 128, 137-138, 311
TOTAL                                       9564     471  95.08%

Diff against main

Filename                    Stmts    Miss  Cover
------------------------  -------  ------  -------
R/formatting_functions.R       +4       0  +0.05%
TOTAL                          +4       0  +0.00%

Results for commit: 151cd13

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

       1 files       80 suites   1m 39s ⏱️
   776 tests    767 ✔️     9 💤 0 ❌
1 645 runs  1 030 ✔️ 615 💤 0 ❌

Results for commit ae10aa8.

♻️ This comment has been updated with latest results.

[anajens]

Thanks @edelarua !

[edelarua]

Notes on implementation:

• Format "fg" is used to format using significant digits - "f" prints with fixed (non-scientific notation) format and "g" causes digits to represent number of significant digits (not decimal places).
• Without the "#" flag, additional required digits are not correctly added and leading whitespace is added instead. For example:

> formatC(signif(1.5, digits = 3), digits = 3, format = "fg", flag = "#")
[1] "1.50"
> formatC(signif(1.5, digits = 3), digits = 3, format = "fg")
[1] " 1.5"

• Without sigfig values are not rounded correctly. For example:

> formatC(signif(123123, digits = 3), digits = 3, format = "fg")
[1] "123000"
> formatC(123123, digits = 3, format = "fg")
[1] "123123"

[Melkiades]

Great job Emily! Thanks for addressing all my doubts :)

[anajens]

@edelarua this is looking a lot better but I think we need to be careful about which formats are supported. I suggest to either restrict the format list more explicitly and/or add more tests to verity that all formats in list_valid_format_labels() are supported:

Here's 2 cases to think about, both seem to be bugs in format_value:

(1) this gives an error:

num1 <- c(0.1239)
z <- format_sigfig(3, format = "xx%" )
z(num1)
>Error in x * 100 : non-numeric argument to binary operator

(2) This gives the wrong result "<0.0001"

num2 <- c(1234)
z <- format_sigfig(3, format = "x.xxxx | (<0.0001)" )
z(num2)

[edelarua]

@anajens I have specified the formats that work in the documentation and added a check in the function.

[anajens]

Thanks, this is much safer 😅