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openpharma / crmPack

Object-Oriented Implementation of CRM Designs
https://openpharma.github.io/crmPack/
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814 implement knit print for subclasses of design #823

Closed Puzzled-Face closed 5 months ago

Puzzled-Face commented 6 months ago

Closes #814.

Please check methods involving Effloglog and LogisticIndepBeta to confirm my interpretation.

github-actions[bot] commented 6 months ago

Unit Tests Summary

    1 files     45 suites   4m 23s :stopwatch: 1 342 tests 1 185 :white_check_mark: 157 :zzz: 0 :x: 6 533 runs  6 338 :white_check_mark: 195 :zzz: 0 :x:

Results for commit 9b38ce47.

:recycle: This comment has been updated with latest results.

github-actions[bot] commented 6 months ago

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
CrmPackClass-class 💚 $32.29$ $-7.74$ $+1$ $0$ $0$ $0$
CrmPackClass-methods 💚 $51.18$ $-1.81$ $+2$ $0$ $0$ $0$
Rules-methods 💔 $29.84$ $+1.01$ $0$ $0$ $0$ $0$
helpers_knitr 💔 $50.11$ $+6.72$ $+66$ $0$ $0$ $0$
helpers_knitr_Design 👶 $+0.94$ $+51$ $0$ $0$ $0$
Additional test case details | Test Suite | $Status$ | Time on `main` | $±Time$ | Test Case | |:-----|:----:|:----:|:----:|:-----| | CrmPackClass-class | 💚 | $32.15$ | $-7.74$ | CrmPackClass_correctly_identifies_crmPack_classes | | CrmPackClass-methods | 💔 | $21.53$ | $+3.11$ | tidy_methods_exist_for_all_relevant_classes | | CrmPackClass-methods | 💚 | $29.66$ | $-4.91$ | tidy_methods_return_non_empty_value_for_all_classes | | helpers_knitr | 💔 | $27.37$ | $+3.24$ | asis_parameter_works_correctly_for_all_implemented_methods | | helpers_knitr | 💔 | $21.94$ | $+3.44$ | knit_print_output_is_suffixed_by_two_newlines_for_all_implemented_methods | | helpers_knitr_Design | 👶 | | $+0.06$ | h_markdown_header_fails_gracefully_with_bad_input | | helpers_knitr_Design | 👶 | | $+0.01$ | h_markdown_header_works_correctly | | helpers_knitr_Design | 👶 | | $+0.02$ | h_prepare_section_labels_works_correctly | | helpers_knitr_Design | 👶 | | $+0.12$ | knit_print_DADesign_works_correctly | | helpers_knitr_Design | 👶 | | $+0.10$ | knit_print_DTDDesign_works_correctly | | helpers_knitr_Design | 👶 | | $+0.10$ | knit_print_Design_works_correctly | | helpers_knitr_Design | 👶 | | $+0.13$ | knit_print_DualDesign_works_correctly | | helpers_knitr_Design | 👶 | | $+0.13$ | knit_print_DualResponsesDesign_works_correctly | | helpers_knitr_Design | 👶 | | $+0.16$ | knit_print_DualResponsesSamplesDesign_works_correctly | | helpers_knitr_Design | 👶 | | $+0.05$ | knit_print_RuleDesignOrdinal_works_correctly | | helpers_knitr_Design | 👶 | | $+0.03$ | knit_print_RuleDesign_works_correctly | | helpers_knitr_Design | 👶 | | $+0.01$ | knit_print_StartingDose_works_correctly | | helpers_knitr_Design | 👶 | | $+0.04$ | v_starting_dose_works_correctly |

Results for commit 65629890e9f71679ef9aec260d8322a6fc6991ee

♻️ This comment has been updated with latest results.

github-actions[bot] commented 6 months ago

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Code Coverage Summary

Filename                          Stmts    Miss  Cover    Missing
------------------------------  -------  ------  -------  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/checkmate.R                        87       2  97.70%   72, 432
R/crmPack-package.R                   4       0  100.00%
R/CrmPackClass-methods.R              5       0  100.00%
R/Data-class.R                      156       5  96.79%   43, 565-566, 572-577
R/Data-methods.R                    267       0  100.00%
R/Data-validity.R                   144       1  99.31%   21
R/Design-class.R                    396       0  100.00%
R/Design-methods.R                 2766     771  72.13%   563-567, 591-594, 602-621, 626-655, 659-660, 662, 677-685, 689, 701-720, 1122-1126, 1253, 1267-1271, 1333, 1523, 1740, 1767-1770, 1779-1790, 1794-1813, 1824-1828, 1834-1846, 2109, 2134-2137, 2144-2155, 2159-2178, 2190-2194, 2200-2212, 2496-2499, 2527-2530, 2538-2550, 2553-2564, 2568-2604, 2621-2630, 2636-2651, 2676, 2717-2718, 2981-3451, 3546-3557, 3560-3571, 3575-3611, 3628-3637, 3645-3660, 3698, 3740-3741, 4020, 4022-4023, 4082, 4118, 4155-4158, 4177-4181, 4242-4249, 4277-4281, 4289-4307, 4333-4352, 4355, 4388, 4410-4428, 4686, 4774
R/Design-validity.R                  34      10  70.59%   47-56
R/fromQuantiles.R                   172      52  69.77%   294-362
R/helpers_broom.R                    74      10  86.49%   30, 34-35, 37-38, 40, 81, 102-104
R/helpers_covr.R                     23       0  100.00%
R/helpers_data.R                     96       1  98.96%   139
R/helpers_design.R                  126      42  66.67%   22, 77-129, 250, 255-259
R/helpers_jags.R                     77       0  100.00%
R/helpers_knitr_CohortSize.R        109       0  100.00%
R/helpers_knitr_Design.R            346       8  97.69%   24-29, 323-324
R/helpers_knitr_GeneralData.R       180      59  67.22%   63-66, 79-82, 95-98, 110-113, 126-129, 151-153, 236-240, 249-294, 341
R/helpers_knitr_GeneralModel.R      730       3  99.59%   105, 401, 813
R/helpers_knitr_Increments.R        165       1  99.39%   297
R/helpers_knitr_NextBest.R          312       0  100.00%
R/helpers_knitr_SafetyWindow.R      142       1  99.30%   103
R/helpers_knitr_Stopping.R          225       0  100.00%
R/helpers_knitr.R                    12       0  100.00%
R/helpers_model.R                    85       4  95.29%   38, 89-90, 139
R/helpers_rules.R                   428       0  100.00%
R/helpers_samples.R                   5       0  100.00%
R/helpers_simulations.R              27       0  100.00%
R/helpers.R                         214      61  71.50%   107-127, 162-178, 200-302, 337-351
R/logger.R                           11       0  100.00%
R/mcmc.R                            290      18  93.79%   92-97, 376-377, 387, 389-390, 393-396, 579-580, 669, 675, 733
R/McmcOptions-class.R                22       0  100.00%
R/McmcOptions-methods.R               8       1  87.50%   43
R/McmcOptions-validity.R             42       0  100.00%
R/Model-class.R                    1062     166  84.37%   145-147, 216-218, 222-224, 283-285, 357-359, 363-365, 444-446, 513-515, 577-581, 584-587, 690-693, 697-698, 813-817, 937-939, 943-951, 1096-1098, 1103-1106, 1110-1113, 1229-1233, 1235-1238, 1242-1245, 1248, 1409-1419, 1424-1430, 1585-1588, 1594-1601, 1758, 1767, 1776, 1785, 1794-1799, 1935, 1944, 1953, 1961-1963, 2807-2836, 2840-2846, 2853-2857, 2862, 2969-2982, 3008, 3104-3106, 3110, 3203-3205, 3209, 3278-3290, 3308, 3368-3370, 3372-3373, 3376-3381
R/Model-methods.R                   505      38  92.48%   78, 233-238, 809-854, 1175-1184
R/Model-validity.R                  443      16  96.39%   430-433, 442-445, 596-604
R/ModelParams-class.R                17       0  100.00%
R/ModelParams-validity.R             21       0  100.00%
R/Rules-class.R                     463       0  100.00%
R/Rules-methods.R                  1561     182  88.34%   889, 892, 895, 1010, 1013, 1016, 1136-1139, 1173, 1276-1279, 1314, 2582-2590, 2614-2621, 2784-2793, 3109-3118, 3251-3494, 3781, 3785
R/Rules-validity.R                  448      30  93.30%   684-723
R/Samples-class.R                     6       0  100.00%
R/Samples-methods.R                1188      21  98.23%   410-420, 648, 1665-1666, 1698, 1711, 1893, 2223-2228
R/Samples-validity.R                 10       0  100.00%
R/Simulations-class.R               208       5  97.60%   759-762, 1019
R/Simulations-methods.R            1617    1473  8.91%    65-350, 406, 416-435, 448-453, 500-509, 674-2969
R/Simulations-validity.R             75      75  0.00%    20-168
R/utils.R                             6       0  100.00%
TOTAL                             15410    3056  80.17%

Diff against main

Filename                          Stmts    Miss  Cover
------------------------------  -------  ------  --------
R/helpers_knitr_CohortSize.R         +4       0  +100.00%
R/helpers_knitr_Design.R           +346      +8  +97.69%
R/helpers_knitr_GeneralData.R        -4      -3  +0.92%
R/helpers_knitr_GeneralModel.R     +182      -4  +0.87%
R/helpers_knitr_Increments.R         +4      -1  +0.64%
R/helpers_knitr_NextBest.R           +2       0  +100.00%
R/helpers_knitr_SafetyWindow.R       -6      -1  +0.65%
R/helpers_knitr_Stopping.R           +3       0  +100.00%
R/helpers_knitr.R                   +12       0  +100.00%
R/Model-methods.R                   +33       0  +0.53%
TOTAL                              +576      -1  +0.78%

Results for commit: 9b38ce473a14d41a3e8b9b7cbc87c074c232cc54

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

Puzzled-Face commented 6 months ago

For the following classes, a bare reference to a class object (for example .DefaultDesign()) generates no output. However, wrapping the reference in knit_print() produces the expected results. I am not sure why.

danielinteractive commented 5 months ago

This PR has been implemented on github.com/openpharma/crmPack. Do not use this PR.

The PR has also been moved. So this is now https://github.com/openpharma/crmPack/pull/823