Individual Loo for submodels

[gowerc]

Closes #402

[github-actions]

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                          34       4  88.24%   52, 396, 416, 471
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                               28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                               3117     121  96.12%

Diff against main

Filename          Stmts    Miss  Cover
--------------  -------  ------  -------
R/JointModel.R       +3       0  +0.18%
TOTAL                +3       0  +0.00%

Results for commit: bb458ad

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

    1 files    178 suites   6m 9s ⏱️
  156 tests   144 ✅ 12 💤 0 ❌
1 091 runs  1 078 ✅ 13 💤 0 ❌

Results for commit bb458ad.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
JointModelSamples	💔	$31.39$	$+1.20$	$0$	$0$	$0$	$0$
brms_compare	👶		$+0.02$	$+1$	$+1$	$0$	$0$
compile	💔	$0.77$	$+2.09$	$0$	$0$	$0$	$0$
extract_quantities	💚	$4.55$	$-1.72$	$0$	$0$	$0$	$0$
misc_models	💔	$4.69$	$+1.39$	$0$	$0$	$0$	$0$
model_multi_chain	💚	$3.13$	$-2.05$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
Grid	💚	$52.46$	$-2.25$	Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
GridPrediction	💔	$123.11$	$+2.76$	GridPrediction_works_as_expected_for_Survival_models
JointModel	👶		$+0.01$	Log_Lik_variables_are_produced_correctly
JointModelSamples	💔	$31.39$	$+1.20$	print_works_as_expected_for_JointModelSamples
LongitudinalQuantiles	💔	$3.48$	$+2.56$	Test_that_LongitudinalQuantities_works_as_expected
SurvivalQuantities	💚	$5.78$	$-1.80$	SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
brms_compare	👶		$+0.07$	jmpost_and_brms_get_similar_loo_for_longitudinal_models
brms_compare	👶		$+0.02$	jmpost_and_brms_get_similar_loo_for_survival_models
compile	💔	$0.77$	$+2.09$	compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
extract_quantities	💚	$4.55$	$-1.72$	extract_quantities_works_as_expected
misc_models	💔	$4.69$	$+1.39$	Longitudinal_Model_doesn_t_print_sampler_rejection_messages
model_multi_chain	💚	$3.13$	$-2.05$	Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
stan_functions	💚	$29.17$	$-1.11$	GSF_SLD_function_works_as_expected

Results for commit 6827661

♻️ This comment has been updated with latest results.

[gowerc]

Actually before merging I think it might be worth adding a few CRON tests that just compare the loo values to that of brms to ensure consistency.

[gowerc]

@gravesti - addressed your comment :) - Also added an URL field to the description file which was throwing up issues for some reason now (probs a package update that I didn't previously have)

[gravesti]

@gowerc I think you might not have pushed your latest changes yet :)

[gowerc]

@gowerc I think you might not have pushed your latest changes yet :)

I think I might have just added that comment on the wrong PR, looking over it I've confused myself now. But the "URL" change looks like it was introduced in the Gamma model PR so maybe I made the change on the wrong branch...

[gowerc]

@gravesti - Looks like merging in main dismissed your approval sorry.