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added missing assertion #311

Merged
merged 1 commit into from
May 8, 2024
Merged

added missing assertion #311

merged 1 commit into from
May 8, 2024

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gowerc
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@gowerc gowerc commented May 7, 2024

No corresponding issue, just realised after I merged the population code that I had forgot to put in the assertion that stops it being used with the SurvivalQuantities as it is not yet defined for them.

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github-actions bot commented May 7, 2024

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Code Coverage Summary

Filename                          Stmts    Miss  Cover    Missing
------------------------------  -------  ------  -------  --------------------------------
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                     77       0  100.00%
R/Grid.R                             32       0  100.00%
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/JointModel.R                      123       8  93.50%   141-143, 193, 197, 239, 285, 291
R/JointModelSamples.R                80       1  98.75%   76
R/Link.R                             62       4  93.55%   200-203
R/LinkComponent.R                    19       3  84.21%   88, 120-121
R/LongitudinalGSF.R                  76       0  100.00%
R/LongitudinalModel.R                19       0  100.00%
R/LongitudinalQuantities.R           67       0  100.00%
R/LongitudinalRandomSlope.R          35       0  100.00%
R/LongitudinalSteinFojo.R            69      20  71.01%   116-147
R/Parameter.R                        14       0  100.00%
R/ParameterList.R                    42       1  97.62%   184
R/Prior.R                           236       8  96.61%   480, 576, 588-606
R/Promise.R                          25       0  100.00%
R/Quantities.R                       60       0  100.00%
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               51       0  100.00%
R/SimLongitudinalRandomSlope.R       42       0  100.00%
R/SimLongitudinalSteinFojo.R         48       0  100.00%
R/SimSurvival.R                     104       0  100.00%
R/StanModel.R                        15       0  100.00%
R/StanModule.R                      179       6  96.65%   199-200, 242, 253, 390, 418
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%   132
R/SurvivalWeibullPH.R                11       0  100.00%
R/brier_score.R                     166       0  100.00%
R/defaults.R                         10       6  40.00%   18-57, 84
R/generics.R                         26       2  92.31%   51, 394
R/link_generics.R                    10       2  80.00%   59, 76
R/settings.R                         12      12  0.00%    55-69
R/utilities.R                       143       1  99.30%   13
R/zzz.R                              28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                              2641     114  95.68%

Diff against main

Filename                  Stmts    Miss  Cover
----------------------  -------  ------  -------
R/SurvivalQuantities.R       +4       0  +0.01%
TOTAL                        +4       0  +0.01%

Results for commit: 7e463c5

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented May 7, 2024

Unit Tests Summary

  1 files   41 suites   10m 24s ⏱️
129 tests  98 ✅ 31 💤 0 ❌
895 runs  864 ✅ 31 💤 0 ❌

Results for commit 7e463c5.

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github-actions bot commented May 7, 2024

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
Grid 💔 $231.28$ $+17.10$ $+1$ $0$ $0$ $0$
LongitudinalQuantiles 💔 $40.53$ $+2.54$ $0$ $0$ $0$ $0$
LongitudinalRandomSlope 💔 $46.40$ $+2.29$ $0$ $0$ $0$ $0$
SurvivalExponential 💔 $26.92$ $+1.52$ $0$ $0$ $0$ $0$
SurvivalLoglogistic 💔 $28.62$ $+2.13$ $0$ $0$ $0$ $0$
SurvivalQuantities 💔 $46.72$ $+2.09$ $0$ $0$ $0$ $0$
SurvivalWeibullPH 💔 $28.28$ $+1.23$ $0$ $0$ $0$ $0$
model_multi_chain 💔 $41.76$ $+3.51$ $0$ $0$ $0$ $0$
stan_functions 💔 $45.81$ $+2.40$ $0$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
Grid 💔 $73.30$ $+5.69$ GridObservered_Constructs_correct_quantities
Grid 👶 $+0.01$ GridPopulation_doesn_t_work_with_SurvivalQuantities
Grid 💔 $36.64$ $+2.95$ GridPopulation_works_as_expected_for_GSF_models
Grid 💔 $28.57$ $+1.89$ GridPopulation_works_as_expected_for_Longitudinal_models
Grid 💔 $92.72$ $+6.56$ Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
LongitudinalQuantiles 💔 $31.80$ $+2.46$ Test_that_LongitudinalQuantities_works_as_expected
LongitudinalRandomSlope 💔 $28.52$ $+1.52$ LongitudinalRandomSlope_correctly_generates_an_intercept_per_study
SurvivalExponential 💔 $26.85$ $+1.52$ SurvivalExponential_can_recover_true_parameter_including_covariates_
SurvivalLoglogistic 💔 $28.48$ $+2.13$ SurvivalLogLogistic_can_recover_known_values
SurvivalQuantities 💔 $38.36$ $+2.02$ SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
SurvivalWeibullPH 💔 $28.20$ $+1.23$ SurvivalWeibullPH_can_recover_known_values
model_multi_chain 💔 $41.76$ $+3.51$ Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains

Results for commit df9125e

♻️ This comment has been updated with latest results.

@gowerc gowerc merged commit 4aa31f9 into main May 8, 2024
19 checks passed
@gowerc gowerc deleted the fix/missing-assertion branch May 8, 2024 09:24
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2 participants