add `h_glm_negbin()` #1163

duanx9 · 2024-01-03T03:22:55Z

Close #856

Implement h_glm_negbin().
Add unit tests.
Update NEWS.md.

github-actions · 2024-01-03T03:29:17Z

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                      195      27  86.15%   206, 224-256, 301-302
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                                      10131     914  90.98%

Diff against main

Filename                   Stmts    Miss  Cover
-----------------------  -------  ------  -------
R/summarize_glm_count.R      +25      -2  +3.21%
TOTAL                        +25      -2  +0.04%

Results for commit: 52764fc

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2024-01-03T03:31:25Z

Unit Tests Summary

1 files 82 suites 1m 6s ⏱️
815 tests 789 ✅ 26 💤 0 ❌
1 725 runs 1 067 ✅ 658 💤 0 ❌

Results for commit 52764fc.

♻️ This comment has been updated with latest results.

github-actions · 2024-01-03T03:31:29Z

Unit Test Performance Difference

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
summarize_glm_count	💀	$0.01$	$-0.01$	glm_count_fails_when_negative_binomial_distribution_is_selected.
summarize_glm_count	👶		$+0.07$	h_glm_negbin_emmeans_fit_works_with_healthy_input
summarize_glm_count	👶		$+0.03$	h_glm_negbin_fails_wrong_inputs
summarize_glm_count	👶		$+0.06$	h_glm_negbin_glm_fit_works_with_healthy_input
summarize_glm_count	👶		$+0.05$	h_glm_poisson_emmeans_fit_works_with_healthy_input_with_covariates
summarize_glm_count	👶		$+0.04$	h_glm_poisson_glm_fit_works_with_healthy_input_with_covariates
summarize_glm_count	👶		$+0.08$	s_glm_count_negative_binomial_works_with_healthy_input
summarize_glm_count	👶		$+0.07$	s_glm_count_negative_binomial_works_with_no_reference_group_selected.
summarize_glm_count	👶		$+0.28$	summarize_glm_count_negative_binomial_works_with_healthy_inputs

Results for commit 22c45fd

♻️ This comment has been updated with latest results.

DESCRIPTION

R/summarize_glm_count.R

tests/testthat/test-summarize_glm_count.R

shajoezhu

Thanks @duanx9 ! I have made some small comments. Cheers

shajoezhu

lgtm! Thanks @duanx9

shajoezhu · 2024-01-03T08:33:19Z

hang on! @duanx9 , let me take another look

shajoezhu

hi @duanx9
I was wondering if you can add more test cases (snapshots), for the negative binomial model, take examples from

testthat::test_that("summarize_glm_count works with healthy inputs", {
testthat::test_that("s_glm_count works with no reference group selected.", {
testthat::test_that("s_glm_count works with healthy input", {

rename previous test with "poisson distribution", and add new ones for "negative binomial"

shajoezhu

Brilliant! Many thanks @duanx9

duanx9 added 2 commits January 2, 2024 08:14

add negbin model to glm_count (#856)

6159dc2

resolve warning from pkg import (#856)

2877e16

duanx9 requested a review from shajoezhu January 3, 2024 03:22

shajoezhu self-assigned this Jan 3, 2024

shajoezhu reviewed Jan 3, 2024

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shajoezhu requested changes Jan 3, 2024

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shajoezhu added the sme label Jan 3, 2024

add minor version dep and improve unit tests for clear comparison (#856)

ea5a014

shajoezhu approved these changes Jan 3, 2024

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shajoezhu and others added 2 commits January 5, 2024 12:56

Merge branch 'main' into 856_glm_negbin@main

13e0e9f

add three more tests for negbin (#856)

52764fc

shajoezhu enabled auto-merge (squash) January 5, 2024 06:50

shajoezhu approved these changes Jan 5, 2024

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shajoezhu merged commit 9f5007a into main Jan 5, 2024
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shajoezhu deleted the 856_glm_negbin@main branch January 5, 2024 06:50

shajoezhu mentioned this pull request Jan 5, 2024

Activate and further test negative binomial functionality #857

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add `h_glm_negbin()` #1163

add `h_glm_negbin()` #1163

duanx9 commented Jan 3, 2024 •

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add h_glm_negbin() #1163

add h_glm_negbin() #1163

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duanx9 commented Jan 3, 2024 • edited Loading

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Code Coverage Summary

Diff against main

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Unit Tests Summary

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Unit Test Performance Difference

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add `h_glm_negbin()` #1163

add `h_glm_negbin()` #1163

duanx9 commented Jan 3, 2024 •

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