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fix brms test #420

Merged
merged 3 commits into from
Sep 17, 2024
Merged

fix brms test #420

merged 3 commits into from
Sep 17, 2024

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gravesti
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@gravesti gravesti commented Sep 5, 2024

  • Add brms:: to prior() call
  • Wrap warnings

@gravesti gravesti requested a review from gowerc September 5, 2024 08:43
@gravesti gravesti linked an issue Sep 5, 2024 that may be closed by this pull request
fix brms::prior in test #419
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github-actions bot commented Sep 5, 2024 •
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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                          33       4  87.88%   52, 382, 402, 457
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                       129      10  92.25%   148-153, 203, 207, 249, 295, 301
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           90       6  93.33%   168-172, 187
R/LongitudinalGSF.R                   95       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             86       5  94.19%   159-163
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        74       0  100.00%
R/SimLongitudinalGSF.R                80       0  100.00%
R/SimLongitudinalRandomSlope.R        42       0  100.00%
R/SimLongitudinalSteinFojo.R          69       0  100.00%
R/SimSurvival.R                      116       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/SurvivalGamma.R                     13       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                 13       0  100.00%
R/utilities.R                        144       2  98.61%   13, 335
R/zzz.R                               29      26  10.34%   4-8, 10-31, 38-47
TOTAL                               3117     122  96.09%

Diff against main

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

Results for commit: 3b72e73

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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Unit Tests Summary

    1 files    178 suites   6m 1s ⏱️
  156 tests   144 ✅ 12 💤 0 ❌
1 091 runs  1 078 ✅ 13 💤 0 ❌

Results for commit 3b72e73.

♻️ This comment has been updated with latest results.

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github-actions bot commented Sep 5, 2024 •
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Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
JointModelSamples 💔 $8.19$ $+22.14$ $0$ $-1$ $0$ $0$
compile 💚 $6.88$ $-2.44$ $0$ $0$ $0$ $0$
extract_quantities 💚 $8.08$ $-6.73$ $0$ $0$ $0$ $0$
misc_models 💚 $11.47$ $-4.33$ $0$ $0$ $0$ $0$
model_multi_chain 💚 $41.63$ $-41.52$ $0$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
Grid 💚 $106.79$ $-59.07$ Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
GridPrediction 💔 $115.77$ $+10.31$ GridPrediction_works_as_expected_for_Survival_models
JointModelSamples 💔 $8.19$ $+22.14$ print_works_as_expected_for_JointModelSamples
LongitudinalClaretBruno 💚 $1638.21$ $-1632.02$ LongitudinalClaretBruno_works_as_expected_with_default_arguments
LongitudinalGSF 💚 $690.47$ $-683.28$ LongitudinalGSF_works_as_expected_with_default_arguments
LongitudinalQuantiles 💚 $41.73$ $-35.58$ Test_that_LongitudinalQuantities_works_as_expected
LongitudinalRandomSlope 💚 $53.13$ $-29.41$ Print_method_for_LongitudinalRandomSlope_works_as_expected
LongitudinalSteinFojo 💚 $1362.73$ $-1355.23$ LongitudinalSteinFojo_works_as_expected_with_default_arguments
SurvivalExponential 💚 $36.46$ $-34.88$ Can_load_and_compile_SurvivalExponential_model
SurvivalGamma 💚 $190.60$ $-189.17$ Print_method_for_SurvivalGamma_works_as_expected
SurvivalLoglogistic 💚 $27.80$ $-26.25$ Can_load_and_compile_SurvivalLogLogistic_model
SurvivalQuantities 💚 $94.84$ $-92.31$ SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
SurvivalWeibullPH 💚 $14.66$ $-13.27$ Print_method_for_SurvivalWeibullPH_works_as_expected
brierScore 💔 $14.47$ $+20.67$ brierScore_SurvivalQuantities_returns_same_results_as_survreg
brms_compare 💚 $170.83$ $-170.75$ jmpost_and_brms_get_similar_loo_for_longitudinal_models
compile 💚 $6.88$ $-2.44$ compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
extract_quantities 💚 $8.08$ $-6.73$ extract_quantities_works_as_expected
misc_models 💚 $11.47$ $-4.33$ Longitudinal_Model_doesn_t_print_sampler_rejection_messages
model_multi_chain 💚 $41.63$ $-41.52$ Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
stan_functions 💚 $33.97$ $-4.74$ GSF_SLD_function_works_as_expected

Results for commit 1d3a624

♻️ This comment has been updated with latest results.

@gowerc gowerc self-requested a review September 17, 2024 10:04
@gowerc gowerc merged commit dbee91c into main Sep 17, 2024
20 checks passed
@gowerc gowerc deleted the 419-fix-brmsprior-in-test branch September 17, 2024 10:06
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fix brms::prior in test
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@gravesti @gowerc