418-population-effects-implementation

[gravesti]

Implements the method as discussed. Closes #418

Would value input on the user options for which terms can be included.

[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                          36       5  86.11%   52, 382, 402, 464, 481
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                       130      11  91.54%   146-151, 201, 205, 247, 293, 299, 322
R/JointModelSamples.R                 71       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                  101       0  100.00%
R/LongitudinalModel.R                 19       0  100.00%
R/LongitudinalQuantities.R            71       0  100.00%
R/LongitudinalRandomEffects.R         53      17  67.92%   80-105
R/LongitudinalRandomSlope.R           45       6  86.67%   102-106, 119
R/LongitudinalSteinFojo.R             91      10  89.01%   159-163, 194-198
R/Parameter.R                         14       0  100.00%
R/ParameterList.R                     42       1  97.62%   184
R/populationHR.R                      44       0  100.00%
R/Prior.R                            270       6  97.78%   547, 691-705
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                               3251     147  95.48%

Diff against main

Filename            Stmts    Miss  Cover
----------------  -------  ------  --------
R/populationHR.R      +44       0  +100.00%
TOTAL                 +44       0  +0.06%

Results for commit: 5e1baa2

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
LongitudinalRandomEffects	💚	$93.42$	$-35.30$	$0$	$0$	$0$	$0$
compile	💚	$11.27$	$-4.87$	$0$	$0$	$0$	$0$
extract_quantities	💚	$13.29$	$-12.52$	$0$	$0$	$0$	$0$
misc_models	💚	$11.61$	$-4.15$	$0$	$0$	$0$	$0$
model_multi_chain	💚	$57.27$	$-45.61$	$0$	$0$	$0$	$0$
populationHR	👶		$+0.00$	$+4$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
Grid	💚	$100.65$	$-58.48$	Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
GridPrediction	💚	$119.69$	$-8.48$	GridPrediction_works_as_expected_for_Survival_models
JointModelSamples	💔	$10.24$	$+20.12$	print_works_as_expected_for_JointModelSamples
LongitudinalClaretBruno	💚	$2181.89$	$-2175.87$	LongitudinalClaretBruno_works_as_expected_with_default_arguments
LongitudinalGSF	💚	$1766.38$	$-1759.43$	LongitudinalGSF_works_as_expected_with_default_arguments
LongitudinalQuantiles	💚	$41.40$	$-36.18$	Test_that_LongitudinalQuantities_works_as_expected
LongitudinalRandomEffects	💚	$93.42$	$-35.30$	LongitudinalRandomEffects_works_as_expected
LongitudinalRandomSlope	💚	$64.52$	$-63.02$	Print_method_for_LongitudinalRandomSlope_works_as_expected
LongitudinalSteinFojo	💚	$1702.83$	$-1702.59$	LongitudinalSteinFojo_works_as_expected_with_default_arguments
SimSurvival	💚	$4.41$	$-1.93$	SimSurvivalExponential_creates_a_dataset_with_the_correct_parameter
SurvivalExponential	💚	$35.47$	$-34.20$	Can_load_and_compile_SurvivalExponential_model
SurvivalGamma	💚	$203.57$	$-203.40$	Print_method_for_SurvivalGamma_works_as_expected
SurvivalLoglogistic	💚	$29.83$	$-28.60$	Can_load_and_compile_SurvivalLogLogistic_model
SurvivalQuantities	💚	$85.88$	$-34.11$	SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
SurvivalWeibullPH	💚	$14.99$	$-13.62$	Print_method_for_SurvivalWeibullPH_works_as_expected
brierScore	💚	$72.01$	$-67.46$	brierScore_SurvivalQuantities_returns_same_results_as_survreg
brms_compare	💚	$346.57$	$-346.51$	jmpost_and_brms_get_similar_loo_for_longitudinal_models
compile	💚	$11.27$	$-4.87$	compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
extract_quantities	💚	$13.29$	$-12.52$	extract_quantities_works_as_expected
misc_models	💚	$11.61$	$-4.15$	Longitudinal_Model_doesn_t_print_sampler_rejection_messages
model_multi_chain	💚	$57.27$	$-45.61$	Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
populationHR	👶		$+0.00$	populationHR_fails_for_bad_input
populationHR	👶		$+0.00$	populationHR_works_as_expected_for_alternative_specfications
populationHR	👶		$+15.41$	populationHR_works_as_expected_for_default_parameters
stan_functions	💚	$41.08$	$-26.99$	GSF_SLD_function_works_as_expected

Results for commit 0271038

♻️ This comment has been updated with latest results.

[danielinteractive]

Thanks a lot @gravesti for tackling this! Please see a few suggestions below

[github-actions]

Unit Tests Summary

    1 files    185 suites   6m 38s ⏱️
  163 tests   151 ✅ 12 💤 0 ❌
1 119 runs  1 106 ✅ 13 💤 0 ❌

Results for commit 5e1baa2.

♻️ This comment has been updated with latest results.

[gravesti]

Thanks for the review @danielinteractive. I've implemented your suggestions.

[danielinteractive]

Nice, thanks a lot Isaac! Also don't forget a NEWS entry for this cool new feature 😉