401 add rate01 tlg@main #739

ayogasekaram · 2022-11-09T19:07:33Z

added unit tests for summarize_glm_count

adding rate01 to tlg MR found here: https://code.roche.com/nest/docs/tlg-catalog/devel/-/merge_requests/162

closes #538

github-actions · 2022-11-09T21:10:25Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      63       0  100.00%
R/abnormal_by_marked.R                        52       5  90.38%   124-128
R/abnormal_by_worst_grade_worsen.R           113       3  97.35%   205-207
R/abnormal_by_worst_grade.R                   37       0  100.00%
R/abnormal.R                                  40       0  100.00%
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        138       3  97.83%   135, 247, 266
R/control_incidence_rate.R                    10       0  100.00%
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                          47       1  97.87%   52
R/count_missed_doses.R                        31       0  100.00%
R/count_occurrences_by_grade.R                84       3  96.43%   148, 163-164
R/count_occurrences.R                         61       1  98.36%   89
R/count_patients_events_in_cols.R             67       0  100.00%
R/count_patients_with_event.R                 72       0  100.00%
R/count_values.R                              24       0  100.00%
R/cox_regression_inter.R                     142       0  100.00%
R/cox_regression.R                           318       0  100.00%
R/coxph.R                                    168       7  95.83%   232-236, 281, 297, 306, 312-313
R/d_pkparam.R                                405       0  100.00%
R/decorate_grob.R                            167       6  96.41%   270-276, 383, 415, 425, 432
R/desctools_binom_diff.R                     668      68  89.82%   65, 100-101, 141-142, 145, 224, 250-261, 300, 302, 322, 326, 330, 334, 386, 389, 392, 395, 456, 464, 476-477, 483-486, 494, 497, 506, 509, 557-558, 560-561, 563-564, 566-567, 640, 652-665, 670, 717, 730, 734
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   53
R/estimate_proportion.R                      198      10  94.95%   421-428, 432, 437, 545
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/footnotes.R                                  5       0  100.00%
R/formats.R                                   88       1  98.86%   66
R/g_forest.R                                 441      42  90.48%   172, 200, 229, 252-253, 257-258, 326, 339, 343-344, 349-350, 363, 379, 426, 457, 533, 542, 614-634, 637, 648, 705, 708, 834
R/g_lineplot.R                               192      29  84.90%   177, 190, 218, 244-247, 320-327, 345-346, 352-362, 458, 466
R/g_step.R                                    68       1  98.53%   106
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        74       0  100.00%
R/h_biomarkers_subgroups.R                    38       0  100.00%
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           74       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   248-261
R/h_stack_by_baskets.R                        65       2  96.92%   96, 143
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           78       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   254-266
R/incidence_rate.R                            93       7  92.47%   69-76
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        532      29  94.55%   256-260, 456, 627-629, 637-639, 665, 672-673, 845, 1030, 1272-1283
R/logistic_regression.R                      569       3  99.47%   279-280, 347
R/missing_data.R                              20       3  85.00%   29, 61, 71
R/odds_ratio.R                               106       0  100.00%
R/prop_diff_test.R                            87       0  100.00%
R/prop_diff.R                                255      11  95.69%   56-63, 190, 364, 508
R/prune_occurrences.R                         57       0  100.00%
R/response_biomarkers_subgroups.R             59       0  100.00%
R/response_subgroups.R                       164       0  100.00%
R/rtables_access.R                            21       0  100.00%
R/score_occurrences.R                         20       1  95.00%   112
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      47       0  100.00%
R/summarize_ancova.R                          94       1  98.94%   197
R/summarize_change.R                          27       0  100.00%
R/summarize_colvars.R                          6       0  100.00%
R/summarize_glm_count.R                      162      34  79.01%   171, 234, 303, 326-359
R/summarize_num_patients.R                    47       3  93.62%   93-95
R/summarize_patients_exposure_in_cols.R       46       0  100.00%
R/summarize_variables_in_cols.R               64       6  90.62%   35, 64, 91, 93, 120, 122
R/summarize_variables.R                      212       1  99.53%   477
R/survival_biomarkers_subgroups.R             59       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   69-77
R/survival_duration_subgroups.R              171       0  100.00%
R/survival_time.R                             47       0  100.00%
R/survival_timepoint.R                       114       7  93.86%   147-153
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                              95       1  98.95%   93
R/utils_grid.R                               111       5  95.50%   150, 260-266
R/utils_rtables.R                             74       2  97.30%   317-318
R/utils.R                                    137      10  92.70%   100, 102, 106, 126, 129, 132, 136, 145-146, 334
R/wrap_text.R                                 65       5  92.31%   37, 58, 78, 85, 107
TOTAL                                       8782     346  96.06%

Diff against main

Filename                   Stmts    Miss  Cover
-----------------------  -------  ------  -------
R/summarize_glm_count.R     +162     +34  +79.01%
TOTAL                       +162     +34  -0.32%

Results for commit: 181aa89

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2022-11-09T21:13:23Z

Unit Tests Summary

      1 files   126 suites 2m 48s ⏱️
  865 tests   865 ✔️ 0 💤 0 ❌
1 304 runs 1 304 ✔️ 0 💤 0 ❌

Results for commit 90d2d29.

♻️ This comment has been updated with latest results.

shajoezhu · 2022-11-10T08:09:45Z

R/summarize_glm_count.R

+#' library(scda)
+#' library(dplyr)
+#' anl <- synthetic_cdisc_dataset("latest", "adtte") %>%
+#'   filter(PARAMCD == "TNE")
+#' anl$AVAL_f <- as.factor(anl$AVAL)


I don't think this part is needed, as the below example is not ran

I think it is needed for the last example which should be on the same doc file. Still, I would not repeat this there

the last example has its own already

shajoezhu · 2022-11-10T08:14:33Z

R/summarize_glm_count.R

+  .null_ref_cells = FALSE
+)
+
+#' @describeIn summarize_glm_count Layout creating function which can be be used for creating


I think we can move from line 411 to the end of function summarize_glm_count to the top of this script, so the documentation is clearer. As all the other parts are internal, and examples won't need to be run.

It makes sense but we can always put comment titles to describe the "internal" steps. Not sure. Maybe you are right and having only "runnable" docs is better

shajoezhu · 2022-11-10T08:16:31Z

tests/testthat/test-summarize_glm_count.R

+  library(scda)
+  library(dplyr)
+  anl <- synthetic_cdisc_dataset("latest", "adtte") %>%
+    filter(PARAMCD == "TNE")
+  anl$AVAL_f <- as.factor(anl$AVAL)


I think this part of data loading can be external to the testing functions. so the testing data can be reused, and will be more efficient.

actually the libraries should be in setup_libraries and the dataset should be taken from the ones in setup_data

Excellent! That is the proper way to do it now! Thanks @Melkiades

shajoezhu

Thanks @ayogasekaram ! it looks really good. I made some samll change requests. thanks!

inst/WORDLIST

Melkiades · 2022-11-10T10:04:57Z

Great job Abi!! :) I did not review it in detail, as Joe is on it, but maybe we could aim at a bit higher coverage (>90%)

…ing/tern into 401_add_rate01_tlg@main

shajoezhu

changes lgtm! Thanks @ayogasekaram

ayogasekaram and others added 6 commits October 26, 2022 21:34

Adding RATE01 functions to tern (summarize_glm_count)

3d09c2d

Adding unit tests for summarize_glm_count functions

71624b2

Merge branch 'main' into 401_add_rate01_tlg@main

b2fd977

Merge b2fd977 into dd92024

35dfc8f

[skip actions] Restyle files

1513368

Updating wordlist and correcting errors

d29693c

Revert roxygen version

d2e50e5

shajoezhu added the sme label Nov 9, 2022

shajoezhu reviewed Nov 10, 2022

View reviewed changes

shajoezhu requested changes Nov 10, 2022

View reviewed changes

shajoezhu self-assigned this Nov 10, 2022

Melkiades reviewed Nov 10, 2022

View reviewed changes

inst/WORDLIST Outdated Show resolved Hide resolved

ayogasekaram and others added 4 commits November 10, 2022 15:49

correcting wordlist. Update test data with setup_data.

4db7ba3

Merge branch '401_add_rate01_tlg@main' of github.com:insightsengineer…

bfa2c0d

…ing/tern into 401_add_rate01_tlg@main

removing unnecessary data load.

a0cedf3

[skip actions] Roxygen Man Pages Auto Update

c986383

shajoezhu mentioned this pull request Nov 11, 2022

Creating additional test to improve converage for rate01 related functions #742

Closed

shajoezhu enabled auto-merge (squash) November 11, 2022 07:11

shajoezhu approved these changes Nov 11, 2022

View reviewed changes

Empty-Commit to trigger cicd

90d2d29

shajoezhu merged commit 98212d3 into main Nov 11, 2022

shajoezhu deleted the 401_add_rate01_tlg@main branch November 11, 2022 07:26

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

401 add rate01 tlg@main #739

401 add rate01 tlg@main #739

ayogasekaram commented Nov 9, 2022

github-actions bot commented Nov 9, 2022 •

edited

Loading

github-actions bot commented Nov 9, 2022 •

edited

Loading

shajoezhu Nov 10, 2022

Melkiades Nov 10, 2022

shajoezhu Nov 10, 2022

shajoezhu Nov 10, 2022

Melkiades Nov 10, 2022

shajoezhu Nov 10, 2022

Melkiades Nov 10, 2022

shajoezhu Nov 10, 2022

shajoezhu left a comment

Melkiades commented Nov 10, 2022

shajoezhu left a comment

401 add rate01 tlg@main #739

401 add rate01 tlg@main #739

Conversation

ayogasekaram commented Nov 9, 2022

github-actions bot commented Nov 9, 2022 • edited Loading

Code Coverage Summary

Diff against main

github-actions bot commented Nov 9, 2022 • edited Loading

Unit Tests Summary

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

shajoezhu left a comment

Choose a reason for hiding this comment

Melkiades commented Nov 10, 2022

shajoezhu left a comment

Choose a reason for hiding this comment

github-actions bot commented Nov 9, 2022 •

edited

Loading

github-actions bot commented Nov 9, 2022 •

edited

Loading