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Genentech / jmpost

https://genentech.github.io/jmpost/
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Multiple variances (Claret) #399

Closed gowerc closed 1 month ago

gowerc commented 1 month ago

Address's the Claret-Bruno part of https://github.com/Genentech/jmpost/issues/389

github-actions[bot] commented 1 month ago

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Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  --------------------------------
R/brier_score.R                      167       0  100.00%
R/DataJoint.R                         76       2  97.37%   264, 270
R/DataLongitudinal.R                 119       1  99.16%   244
R/DataSubject.R                       85       1  98.82%   142
R/DataSurvival.R                      98       0  100.00%
R/defaults.R                          10       6  40.00%   18-57, 84
R/generics.R                          34       4  88.24%   52, 396, 416, 471
R/Grid.R                              27       1  96.30%   173
R/GridEven.R                          32       0  100.00%
R/GridEvent.R                         22       0  100.00%
R/GridFixed.R                         30       0  100.00%
R/GridGrouped.R                       52       0  100.00%
R/GridManual.R                        23       3  86.96%   78-80
R/GridObserved.R                      20       0  100.00%
R/GridPopulation.R                    31       4  87.10%   61, 69-71
R/GridPrediction.R                    36       6  83.33%   83, 91-95
R/JointModel.R                       126      10  92.06%   146-151, 201, 205, 247, 293, 299
R/JointModelSamples.R                 66       0  100.00%
R/link_generics.R                     16       4  75.00%   59, 76, 91, 106
R/Link.R                              62       4  93.55%   200-203
R/LinkComponent.R                     19       3  84.21%   88, 120-121
R/LongitudinalClaretBruno.R           89       6  93.26%   164-168, 183
R/LongitudinalGSF.R                   94       0  100.00%
R/LongitudinalModel.R                 19       0  100.00%
R/LongitudinalQuantities.R            71       0  100.00%
R/LongitudinalRandomSlope.R           44       5  88.64%   102-106
R/LongitudinalSteinFojo.R             85       5  94.12%   155-159
R/Parameter.R                         14       0  100.00%
R/ParameterList.R                     42       1  97.62%   184
R/Prior.R                            254       6  97.64%   507, 651-665
R/Promise.R                           25       0  100.00%
R/Quantities.R                        60       0  100.00%
R/QuantityGeneratorPopulation.R       22       0  100.00%
R/QuantityGeneratorPrediction.R       48       0  100.00%
R/QuantityGeneratorSubject.R          19       0  100.00%
R/settings.R                          12      12  0.00%    55-69
R/SimGroup.R                           5       0  100.00%
R/SimJointData.R                      72       1  98.61%   103
R/SimLongitudinal.R                    5       2  60.00%   22, 40
R/SimLongitudinalClaretBruno.R        72       0  100.00%
R/SimLongitudinalGSF.R                62       0  100.00%
R/SimLongitudinalRandomSlope.R        42       0  100.00%
R/SimLongitudinalSteinFojo.R          52       0  100.00%
R/SimSurvival.R                      104       0  100.00%
R/StanModel.R                         15       0  100.00%
R/StanModule.R                       176       6  96.59%   192-193, 235, 246, 383, 411
R/SurvivalExponential.R               10       0  100.00%
R/SurvivalLoglogistic.R               11       0  100.00%
R/SurvivalModel.R                     19       0  100.00%
R/SurvivalQuantities.R               170       1  99.41%   125
R/SurvivalWeibullPH.R                 11       0  100.00%
R/utilities.R                        144       2  98.61%   13, 335
R/zzz.R                               28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                               3047     121  96.03%

Diff against main

Filename                          Stmts    Miss  Cover
------------------------------  -------  ------  --------
R/SimLongitudinalClaretBruno.R      +20       0  +100.00%
TOTAL                               +20       0  +0.03%

Results for commit: a545be42ada861814d198c2aea9f1c1db4ba6214

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

github-actions[bot] commented 1 month ago

Unit Tests Summary

    1 files    162 suites   6m 30s :stopwatch:   140 tests   137 :white_check_mark: 3 :zzz: 0 :x: 1 059 runs  1 055 :white_check_mark: 4 :zzz: 0 :x:

Results for commit a545be42.

github-actions[bot] commented 1 month ago

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
JointModelSamples 💔 $10.11$ $+21.89$ $0$ $-1$ $0$ $0$
compile 💚 $10.56$ $-4.98$ $0$ $0$ $0$ $0$
extract_quantities 💚 $12.33$ $-12.17$ $0$ $0$ $0$ $0$
misc_models 💚 $11.68$ $-1.46$ $0$ $0$ $0$ $0$
model_multi_chain 💚 $56.53$ $-29.02$ $0$ $0$ $0$ $0$
Additional test case details | Test Suite | $Status$ | Time on `main` | $±Time$ | Test Case | |:-----|:----:|:----:|:----:|:-----| | Grid | 💚 | $109.58$ | $-59.55$ | Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser | | GridPrediction | 💔 | $121.76$ | $+1.34$ | GridPrediction_works_as_expected_for_Survival_models | | JointModelSamples | 💔 | $10.11$ | $+21.89$ | print_works_as_expected_for_JointModelSamples | | LongitudinalClaretBruno | 💚 | $1195.30$ | $-1189.84$ | LongitudinalClaretBruno_works_as_expected_with_default_arguments | | LongitudinalGSF | 💚 | $448.63$ | $-442.29$ | LongitudinalGSF_works_as_expected_with_default_arguments | | LongitudinalQuantiles | 💚 | $55.35$ | $-47.48$ | Test_that_LongitudinalQuantities_works_as_expected | | LongitudinalRandomSlope | 💚 | $72.42$ | $-67.72$ | Print_method_for_LongitudinalRandomSlope_works_as_expected | | LongitudinalSteinFojo | 💚 | $1442.36$ | $-1435.60$ | LongitudinalSteinFojo_works_as_expected_with_default_arguments | | SurvivalExponential | 💚 | $27.14$ | $-3.74$ | SurvivalExponential_can_recover_true_parameter_including_covariates_ | | SurvivalLoglogistic | 💚 | $29.64$ | $-9.57$ | sim_os_loglogistic_is_consistant_with_flexsurv | | SurvivalQuantities | 💚 | $80.04$ | $-78.89$ | SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected | | SurvivalWeibullPH | 💚 | $11.74$ | $-3.11$ | Print_method_for_SurvivalWeibullPH_works_as_expected | | brierScore | 💔 | $19.18$ | $+17.92$ | brierScore_SurvivalQuantities_returns_same_results_as_survreg | | compile | 💚 | $10.56$ | $-4.98$ | compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist | | extract_quantities | 💚 | $12.33$ | $-12.17$ | extract_quantities_works_as_expected | | misc_models | 💚 | $11.68$ | $-1.46$ | Longitudinal_Model_doesn_t_print_sampler_rejection_messages | | model_multi_chain | 💚 | $56.53$ | $-29.02$ | Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains | | stan_functions | 💚 | $39.44$ | $-38.93$ | GSF_SLD_function_works_as_expected |

Results for commit e040ba462420636d189a9c79f7c49e3656ccb8bc

♻️ This comment has been updated with latest results.