Refactor `g_forest` #1158

edelarua · 2023-12-08T23:02:11Z

Pull Request

Part of #1109

g_forest creates a ggplot object instead of a grob object.

github-actions · 2023-12-08T23:17:55Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      68       2  97.06%   78-79
R/abnormal_by_marked.R                        55       5  90.91%   78-82
R/abnormal_by_worst_grade_worsen.R           116       3  97.41%   240-242
R/abnormal_by_worst_grade.R                   60       0  100.00%
R/abnormal.R                                  43       0  100.00%
R/analyze_variables.R                        190      10  94.74%   489-490, 506, 530, 686-687, 692-693, 711-712
R/analyze_vars_in_cols.R                     179      35  80.45%   168-169, 184, 207-212, 227, 241-242, 250-258, 264-270, 349-355
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        124      17  86.29%   131-135, 247, 325-334, 389-390, 396
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                          50       1  98.00%   67
R/count_missed_doses.R                        34       0  100.00%
R/count_occurrences_by_grade.R               107       4  96.26%   144-146, 149
R/count_occurrences.R                        115       1  99.13%   108
R/count_patients_events_in_cols.R             67       1  98.51%   53
R/count_patients_with_event.R                 47       0  100.00%
R/count_patients_with_flags.R                 58       4  93.10%   56-57, 62-63
R/count_values.R                              27       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                            173      40  76.88%   235-266, 326-328, 339, 360-397
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                  50       1  98.00%   63
R/estimate_proportion.R                      205      12  94.15%   78-85, 89, 94, 315, 482, 588
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     181       3  98.34%   145, 155, 280
R/g_forest.R                                 571     412  27.85%   183-186, 189-192, 195-201, 204-207, 210-213, 240, 252-255, 260-261, 277, 287-290, 337-340, 347, 416, 493-1013
R/g_lineplot.R                               206      34  83.50%   168, 181, 210, 236-239, 315-322, 340-341, 347-357, 449, 455, 457, 499-500, 504-505
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                    45       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           76       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           81       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                            96       7  92.71%   44-51
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        688      65  90.55%   236-239, 279-314, 323-327, 538, 725-727, 735-737, 769-770, 943-946, 1169, 1495-1506
R/logistic_regression.R                      102       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               109       0  100.00%
R/prop_diff_test.R                            91       0  100.00%
R/prop_diff.R                                265      16  93.96%   62-65, 97, 282-289, 432, 492, 597
R/prune_occurrences.R                         57      10  82.46%   138-142, 188-192
R/response_biomarkers_subgroups.R             61       0  100.00%
R/response_subgroups.R                       185       4  97.84%   267, 315-317
R/riskdiff.R                                  59       7  88.14%   102-105, 114, 124-125
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                         101       1  99.01%   172
R/summarize_change.R                          30       0  100.00%
R/summarize_colvars.R                         13       2  84.62%   72-73
R/summarize_coxreg.R                         178       6  96.63%   201-202, 209, 346-347, 442
R/summarize_glm_count.R                      170      29  82.94%   160, 164-214, 259-260
R/summarize_num_patients.R                    99       9  90.91%   108-110, 160-161, 252-257
R/summarize_patients_exposure_in_cols.R       96       1  98.96%   42
R/survival_biomarkers_subgroups.R             63       0  100.00%
R/survival_coxph_pairwise.R                   76       9  88.16%   51-59
R/survival_duration_subgroups.R              184       0  100.00%
R/survival_time.R                             79       0  100.00%
R/survival_timepoint.R                       113       7  93.81%   120-126
R/utils_checkmate.R                           68       0  100.00%
R/utils_default_stats_formats_labels.R       136       4  97.06%   72, 577-580
R/utils_factor.R                             109       2  98.17%   84, 302
R/utils_ggplot.R                              72       0  100.00%
R/utils_grid.R                               111       5  95.50%   149, 258-264
R/utils_rtables.R                            100       9  91.00%   39, 46, 51, 58-62, 403-404
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                                      10106     916  90.94%

Diff against main

Filename            Stmts    Miss  Cover
----------------  -------  ------  --------
R/g_forest.R         +133    +391  -67.36%
R/utils_ggplot.R       +4     -68  +100.00%
TOTAL                +137    +323  -3.12%

Results for commit: 469d2b7

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-12-08T23:20:11Z

Unit Tests Summary

      1 files     82 suites 1m 5s ⏱️
  808 tests   782 ✔️   26 💤 0 ❌
1 710 runs 1 059 ✔️ 651 💤 0 ❌

Results for commit 469d2b7.

♻️ This comment has been updated with latest results.

github-actions · 2023-12-08T23:20:15Z

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
g_forest	💔	$1.03$	$+1.01$	$+1$	$+1$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
g_forest	👶		$+0.70$	g_forest_as_list_argument_works
utils_ggplot	👶		$+0.25$	rtable2gg_works_as_expected
utils_ggplot	👶		$+0.52$	rtable2gg_works_with_multiple_column_splits
utils_ggplot	💀	$0.12$	$-0.12$	rtables2gg_works_as_expected
utils_ggplot	💀	$0.10$	$-0.10$	rtables2gg_works_with_multiple_column_splits

Results for commit 8aa4253

♻️ This comment has been updated with latest results.

shajoezhu

looks really good! Thanks @edelarua

shajoezhu · 2023-12-14T00:09:13Z

hi @edelarua , can you introduce this changes in tern.gee and tern.mmrm as well please. thanks!

edelarua · 2023-12-14T00:29:22Z

hi @edelarua , can you introduce this changes in tern.gee and tern.mmrm as well please. thanks!

Hi @shajoezhu,
tern.gee doesn't use g_forest anywhere currently. I checked tern.mmrm and no changes are needed, we'll just have to update the tern version dependency at some point to use the new version. I will check if chevron needs updates tomorrow!

shajoezhu · 2023-12-14T01:37:28Z

Hi @edelarua , it was requested before, but held it because i was wanted to change the gforest implmentation, and you did it! :)

we can create another issue, and follow up on this again, basically would be the same as from tern.mmrm

shajoezhu · 2023-12-14T04:40:11Z

Downstream, we will need to update scda.test and tlg.c as well. Thanks!

Closes #86 Merge after insightsengineering/tern#1158 --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Closes #182 Merge after insightsengineering/tern#1158 This should standardize the generation of graph snapshots across different systems and hopefully fix the failing integration tests for graph snapshot differences. Note: kmg01 snapshots will be fixed after `g_km` is refactored. --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Closes #715 Merge after chevron release and insightsengineering/tern#1158 --------- Signed-off-by: Emily de la Rua <[email protected]> Co-authored-by: benoit <[email protected]> Co-authored-by: Liming <[email protected]>

edelarua added 16 commits December 5, 2023 10:47

Merge branch 'main' into g_forest@main

983cf9f

temp

a5577c0

Update params

663883f

Fix overlaid text labels in rtable2gg

f8087c4

Add missing params

e98089e

Replace old g_forest function

41062fe

Update docs

39dbde8

Merge branch 'main' into 1109_refactor_g_forest@main

e1330f5

Add function to test setup to process ggplot snapshots

5136908

Update rtable2gg tests

a989863

Update existing g_forest tests

4c14287

Update documentation

120029f

Adjust panel background

244001d

Add tests

aecab2c

Clean up aesthetics

01cad41

Update NEWS

02c376a

edelarua added the sme label Dec 8, 2023

edelarua added 2 commits December 8, 2023 18:06

Update NEWS

5e5d0af

Make plot background transparent

1e4e32b

shajoezhu approved these changes Dec 13, 2023

View reviewed changes

shajoezhu self-assigned this Dec 13, 2023

walkowif and others added 6 commits December 13, 2023 10:28

Workflow propagation (#1159)

42ac9b0

[skip actions] Bump version to 0.9.3.9001

16a82a6

Add as_list arg to store table and plot in a list instead of printing

641e18d

Adjust x axis text size

d77d056

Convert to standard font sizes, remove overlaid segment elements

56e1ee6

Change font size scaling, fix overlaid line segments

5ea92c5

Update docs

8cd04b3

edelarua mentioned this pull request Dec 13, 2023

Update forest plot modules following refactor of g_forest insightsengineering/teal.modules.clinical#910

Closed

edelarua and others added 3 commits December 13, 2023 23:50

Merge 8cd04b3 into 16a82a6

93c3952

[skip actions] Restyle files

34f383a

Empty commit

160ee71

edelarua mentioned this pull request Dec 13, 2023

Investigate feasibility of exclusively using ggplot2 for all plots #1109

Closed

2 tasks

Fix segment scale after changing from geom_segment to annotate

2b6a4f8

Last fixes for log scaling

bcb44c9

Refresh test snapshots

469d2b7

shajoezhu merged commit ccbc10c into main Dec 20, 2023
24 checks passed

shajoezhu deleted the 1109_refactor_g_forest@main branch December 20, 2023 04:19

edelarua mentioned this pull request Jan 2, 2024

g_forest() clipping the output #73

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Refactor `g_forest` #1158

Refactor `g_forest` #1158

edelarua commented Dec 8, 2023

github-actions bot commented Dec 8, 2023 •

edited

Loading

github-actions bot commented Dec 8, 2023 •

edited

Loading

github-actions bot commented Dec 8, 2023 •

edited

Loading

shajoezhu left a comment

shajoezhu commented Dec 14, 2023

edelarua commented Dec 14, 2023

shajoezhu commented Dec 14, 2023 •

edited

Loading

shajoezhu commented Dec 14, 2023

Refactor g_forest #1158

Refactor g_forest #1158

Conversation

edelarua commented Dec 8, 2023

Pull Request

github-actions bot commented Dec 8, 2023 • edited Loading

Code Coverage Summary

Diff against main

github-actions bot commented Dec 8, 2023 • edited Loading

Unit Tests Summary

github-actions bot commented Dec 8, 2023 • edited Loading

Unit Test Performance Difference

shajoezhu left a comment

Choose a reason for hiding this comment

shajoezhu commented Dec 14, 2023

edelarua commented Dec 14, 2023

shajoezhu commented Dec 14, 2023 • edited Loading

shajoezhu commented Dec 14, 2023

Refactor `g_forest` #1158

Refactor `g_forest` #1158

github-actions bot commented Dec 8, 2023 •

edited

Loading

github-actions bot commented Dec 8, 2023 •

edited

Loading

github-actions bot commented Dec 8, 2023 •

edited

Loading

shajoezhu commented Dec 14, 2023 •

edited

Loading