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Genentech / jmpost

https://genentech.github.io/jmpost/
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Fix failing CRON unit tests #336

Closed gowerc closed 5 months ago

gowerc commented 5 months ago

Closes #333

Not really sure what the problem was, I think just noise so I tightened the model a bit (use exponential instead of weibull) used more spaced out numbers, added a few more subjects and samples. Seems to be working locally now.

github-actions[bot] commented 5 months ago

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Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  --------------------------------
R/brier_score.R                      166       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                          31       4  87.10%   51, 395, 414, 449
R/Grid.R                              27       1  96.30%   170
R/GridEven.R                          32       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                       123       8  93.50%   141-143, 193, 197, 239, 285, 291
R/JointModelSamples.R                 59       0  100.00%
R/link_generics.R                     13       3  76.92%   59, 76, 91
R/Link.R                              62       4  93.55%   200-203
R/LinkComponent.R                     19       3  84.21%   88, 120-121
R/LongitudinalGSF.R                   82       0  100.00%
R/LongitudinalModel.R                 19       0  100.00%
R/LongitudinalQuantities.R            71       0  100.00%
R/LongitudinalRandomSlope.R           41       5  87.80%   93-97
R/LongitudinalSteinFojo.R             75       5  93.33%   143-147
R/Parameter.R                         14       0  100.00%
R/ParameterList.R                     42       1  97.62%   184
R/Prior.R                            236       8  96.61%   481, 577, 589-607
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/SimLongitudinalGSF.R                53       0  100.00%
R/SimLongitudinalRandomSlope.R        42       0  100.00%
R/SimLongitudinalSteinFojo.R          50       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                        143       1  99.30%   13
R/zzz.R                               28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                               2792     113  95.95%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 1e6ad37829a69263798838daf6e2dcf5dd2f1bfb

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

github-actions[bot] commented 5 months ago

Unit Tests Summary

  1 files  140 suites   6m 54s :stopwatch: 131 tests 104 :white_check_mark: 27 :zzz: 0 :x: 929 runs  897 :white_check_mark: 32 :zzz: 0 :x:

Results for commit 1e6ad378.

github-actions[bot] commented 5 months ago

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
compile 💚 $14.86$ $-9.30$ $0$ $0$ $0$ $0$
extract_quantities 💚 $16.45$ $-9.29$ $0$ $0$ $0$ $0$
model_multi_chain 💚 $70.83$ $-30.41$ $0$ $0$ $0$ $0$
Additional test case details | Test Suite | $Status$ | Time on `main` | $±Time$ | Test Case | |:-----|:----:|:----:|:----:|:-----| | Grid | 💚 | $152.80$ | $-113.62$ | Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser | | GridPrediction | 💔 | $150.53$ | $+4.40$ | GridPrediction_works_as_expected_for_Survival_models | | LongitudinalGSF | 💚 | $5.26$ | $-3.24$ | LongitudinalGSF_works_as_expected_with_default_arguments | | LongitudinalQuantiles | 💔 | $30.09$ | $+13.45$ | Test_that_LongitudinalQuantities_works_as_expected | | LongitudinalRandomSlope | 💚 | $56.89$ | $-54.61$ | Print_method_for_LongitudinalRandomSlope_works_as_expected | | LongitudinalSteinFojo | 💚 | $375.02$ | $-372.25$ | LongitudinalSteinFojo_works_as_expected_with_default_arguments | | SurvivalLoglogistic | 💚 | $46.34$ | $-42.10$ | sim_os_loglogistic_is_consistant_with_flexsurv | | SurvivalQuantities | 💚 | $79.88$ | $-70.77$ | SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected | | SurvivalWeibullPH | 💚 | $10.09$ | $-2.62$ | Print_method_for_SurvivalWeibullPH_works_as_expected | | brierScore | 💔 | $3.32$ | $+31.30$ | brierScore_SurvivalQuantities_returns_same_results_as_survreg | | compile | 💚 | $14.86$ | $-9.30$ | compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist | | extract_quantities | 💚 | $16.45$ | $-9.29$ | extract_quantities_works_as_expected | | model_multi_chain | 💚 | $70.83$ | $-30.41$ | Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains | | stan_functions | 💚 | $68.32$ | $-57.86$ | GSF_SLD_function_works_as_expected |

Results for commit 8bb4dd3afe5760d6929fecfa22f287c041d5be0c

♻️ This comment has been updated with latest results.