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removed legacy option #335

Merged
merged 2 commits into from
Jun 5, 2024
Merged

removed legacy option #335

merged 2 commits into from
Jun 5, 2024

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gowerc
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@gowerc gowerc commented Jun 5, 2024

Closes #332

Removes a historic option from the code as the option is never actually set / used.

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github-actions bot commented Jun 5, 2024

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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: 90af5ad

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Jun 5, 2024

Unit Tests Summary

  1 files  140 suites   6m 52s ⏱️
131 tests 104 ✅ 27 💤 0 ❌
929 runs  897 ✅ 32 💤 0 ❌

Results for commit 90af5ad.

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github-actions bot commented Jun 5, 2024

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
compile 💚 $14.86$ $-6.81$ $0$ $0$ $0$ $0$
extract_quantities 💚 $16.45$ $-11.77$ $0$ $0$ $0$ $0$
model_multi_chain 💚 $70.83$ $-28.49$ $0$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
Grid 💚 $152.80$ $-114.48$ Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
GridPrediction 💔 $150.53$ $+3.88$ GridPrediction_works_as_expected_for_Survival_models
LongitudinalGSF 💚 $5.26$ $-3.28$ LongitudinalGSF_works_as_expected_with_default_arguments
LongitudinalQuantiles 💔 $30.09$ $+13.32$ Test_that_LongitudinalQuantities_works_as_expected
LongitudinalRandomSlope 💚 $56.89$ $-52.37$ Print_method_for_LongitudinalRandomSlope_works_as_expected
LongitudinalSteinFojo 💚 $375.02$ $-372.13$ LongitudinalSteinFojo_works_as_expected_with_default_arguments
SurvivalExponential 💚 $26.77$ $-2.86$ SurvivalExponential_can_recover_true_parameter_including_covariates_
SurvivalLoglogistic 💚 $46.34$ $-39.85$ sim_os_loglogistic_is_consistant_with_flexsurv
SurvivalQuantities 💚 $79.88$ $-73.28$ SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
SurvivalWeibullPH 💚 $10.09$ $-2.46$ Print_method_for_SurvivalWeibullPH_works_as_expected
brierScore 💔 $3.32$ $+30.21$ brierScore_SurvivalQuantities_returns_same_results_as_survreg
compile 💚 $14.86$ $-6.81$ compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
extract_quantities 💚 $16.45$ $-11.77$ extract_quantities_works_as_expected
model_multi_chain 💚 $70.83$ $-28.49$ Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
stan_functions 💚 $68.32$ $-59.72$ GSF_SLD_function_works_as_expected

Results for commit fee2490

♻️ This comment has been updated with latest results.

@gowerc gowerc merged commit c76d738 into main Jun 5, 2024
4 of 16 checks passed
@gowerc gowerc deleted the 332-remove-legacy-option branch June 5, 2024 15:50
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Update gauss.quad code to not use undefined variable
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