Re-factored the stan code for longitudinal generated quantities

[gowerc]

Addresses part 1 of #288

In this PR I factor out the looping code into the base longitudinal model stan file. This means each individual model doesn't have to concern itself about how patients are subset meaning less chance of issues in the future when we update this mechanism.

We then introduce a new interface that the longitudinal models have to conform to which is that they must create a function with signature:

row_vector lm_predict_individual_patient(vector time, row_vector long_gq_parameters)

They also must define a matrix long_gq_parameters which has 1 row per patient and as many columns as required for the model in question. As an example for the SF model this is defined as:

    matrix[Nind, 3] long_gq_parameters;
    long_gq_parameters[, 1] = lm_gsf_psi_bsld;
    long_gq_parameters[, 2] = lm_gsf_psi_ks;
    long_gq_parameters[, 3] = lm_gsf_psi_kg;

I also added a new unit test to show that patient subsetting works as expected and that the correct values are reconstructed per each sample per patient.

[github-actions]

Unit Tests Summary

  1 files   40 suites   5m 30s ⏱️
121 tests  90 ✅ 31 💤 0 ❌
850 runs  819 ✅ 31 💤 0 ❌

Results for commit f5a0403.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
LongitudinalQuantiles	💚	$44.63$	$-2.71$	$+1$	$0$	$0$	$0$
SurvivalLoglogistic	💚	$30.77$	$-1.25$	$0$	$0$	$0$	$0$
compile	💚	$16.20$	$-2.40$	$0$	$0$	$0$	$0$
stan_functions	💚	$50.10$	$-2.92$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
LongitudinalQuantiles	👶		$+0.92$	LongitudinalQuantities_correctly_subsets_patients_and_rebuilds_correct_value_for_each_sample
LongitudinalQuantiles	💚	$37.26$	$-3.73$	Test_that_LongitudinalQuantities_works_as_expected
SurvivalLoglogistic	💚	$30.59$	$-1.24$	SurvivalLogLogistic_can_recover_known_values
compile	💚	$16.20$	$-2.40$	compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
stan_functions	💚	$17.79$	$-2.52$	GSF_SLD_function_works_as_expected

Results for commit 835c5b9

♻️ This comment has been updated with latest results.

[github-actions]

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%   245
R/DataSubject.R                      69       1  98.55%   124
R/DataSurvival.R                     77       0  100.00%
R/defaults.R                         10       6  40.00%   18-57, 84
R/generics.R                         23       1  95.65%   49
R/JointModel.R                      122       8  93.44%   142-144, 194, 198, 240, 286, 292
R/JointModelSamples.R                55       0  100.00%
R/Link.R                             55       4  92.73%   159-162
R/LinkComponent.R                    47       5  89.36%   100, 118, 132-149
R/LongitudinalGSF.R                  64       0  100.00%
R/LongitudinalModel.R                37      12  67.57%   71-86
R/LongitudinalQuantities.R           85       0  100.00%
R/LongitudinalRandomSlope.R          27       0  100.00%
R/LongitudinalSteinFojo.R            57       8  85.96%   113-135
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/Quantities.R                      105       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               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              155       6  96.13%   178-183
R/SurvivalWeibullPH.R                11       0  100.00%
R/utilities.R                       145       1  99.31%   13
R/zzz.R                               2       2  0.00%    3-12
TOTAL                              2372      87  96.33%

Diff against main

Filename                      Stmts    Miss  Cover
--------------------------  -------  ------  -------
R/LongitudinalModel.R            +2       0  +1.85%
R/LongitudinalQuantities.R        0      -8  +9.41%
R/StanModule.R                   +2       0  +0.04%
TOTAL                            +4      -8  +0.34%

Results for commit: f5a0403

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results