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Genentech / jmpost

https://genentech.github.io/jmpost/
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Harmonise Simulation and formula parameter values #354

Closed gowerc closed 5 months ago

gowerc commented 5 months ago

Closes #349

Bit of a deviation from the original issue. The initial values are indeed correct but there was a bit of inconsistency that the model and formulas were specifying the raw value but the simulation functions were specifying the exp(value). I've updated the simulation functions to specify the raw value so that everything is consistent.

Sorry to re-explain that I originally thought the initial values were wrong because they were so wildly different to the values I was specifying in the simulation function. But they aren't wrong they are just on different scales which is confusing so I have harmonised the scales.

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%   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                       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                               2814     113  95.98%

Diff against main

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

Results for commit: 2306065191634f31478bba9ffe5a69d0e9df74ae

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

github-actions[bot] commented 5 months ago

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
JointModelSamples 💔 $33.34$ $+1.79$ $0$ $0$ $0$ $0$
Additional test case details | Test Suite | $Status$ | Time on `main` | $±Time$ | Test Case | |:-----|:----:|:----:|:----:|:-----| | Grid | 💔 | $39.79$ | $+1.16$ | Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser | | GridPrediction | 💔 | $152.08$ | $+4.47$ | GridPrediction_works_as_expected_for_Survival_models | | JointModelSamples | 💔 | $33.34$ | $+1.79$ | print_works_as_expected_for_JointModelSamples | | LongitudinalQuantiles | 💔 | $42.78$ | $+1.17$ | Test_that_LongitudinalQuantities_works_as_expected |

Results for commit a9be1f5241ba6e21f9cef5699f4ab06a562b6f46

♻️ This comment has been updated with latest results.

github-actions[bot] commented 5 months ago

Unit Tests Summary

  1 files  140 suites   7m 25s :stopwatch: 131 tests 104 :white_check_mark: 27 :zzz: 0 :x: 934 runs  902 :white_check_mark: 32 :zzz: 0 :x:

Results for commit 23060651.

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