Fix SF Quantities

[gowerc]

Closes #368

Ok so the actual bug fix was trivial was just a case of fixing a simple typo e.g. gsf -> sf. What was a bit more involved though was updating the unit tests to actually catch this error. It would have been easy to just compile all of the models but this would have added a ton of run time especially if we want to test each permutation of model / quantity generation.

Instead I decided to abstract the code that generates the StanModule for the quantities into its own function so that we can just grab that object before its actually compiled. I then put together a mock JointModelSamples object to which I then use to generate the corresponding StanModule and then run the stan parser to make sure theres no obviously variable errors.

I then added the unit test to our other longitudinal models to make sure no other bugs like this exist.

A bit of a red herring in these changes was that my original implementation tried to expand on the write_stan() function. I adapted the function to take a connection stream to which I was going to pipe the output to a variable. I abandoned this implementation for testing this PR but I thought having the function take a stream was a nice change so left it in as I had already written the code (hope thats ok).

[gowerc]

@gravesti - The "files changed" tab on GitHub here is miss-leading; as I've moved a chunk of code (without modification) between 2 functions the diff is just showing the difference between the code chunks immediately before the chunk I moved. I would potentially recommend viewing the complete file and not just the diff.

[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                          33       4  87.88%   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                       126      10  92.06%   146-151, 201, 205, 247, 293, 299
R/JointModelSamples.R                 66       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/LongitudinalClaretBruno.R           83       6  92.77%   156-160, 175
R/LongitudinalGSF.R                   83       0  100.00%
R/LongitudinalModel.R                 19       0  100.00%
R/LongitudinalQuantities.R            71       0  100.00%
R/LongitudinalRandomSlope.R           42       5  88.10%   98-102
R/LongitudinalSteinFojo.R             76       5  93.42%   149-153
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/SimLongitudinalClaretBruno.R        52       0  100.00%
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                        144       2  98.61%   13, 335
R/zzz.R                               28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                               2966     122  95.89%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/JointModel.R                  +1      +2  -1.54%
R/JointModelSamples.R           +3       0  +100.00%
R/LongitudinalSteinFojo.R        0      -1  +1.32%
R/utilities.R                   +1      +1  -0.69%
TOTAL                           +5      +2  -0.06%

Results for commit: 627b514

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[gravesti]

Looks good to me, @gowerc
just one bug I think

[gowerc]

Updated to add the same test for the new claretBruno model which was merged in this morning

[github-actions]

Unit Tests Summary

    1 files    154 suites   6m 44s ⏱️
  136 tests   133 ✅ 3 💤 0 ❌
1 021 runs  1 017 ✅ 4 💤 0 ❌

Results for commit 627b514.

♻️ 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	💚	$32.29$	$-1.47$	$0$	$0$	$0$	$0$
compile	💚	$6.56$	$-5.45$	$0$	$0$	$0$	$0$
extract_quantities	💔	$0.87$	$+2.38$	$0$	$0$	$0$	$0$
model_multi_chain	💚	$7.88$	$-2.29$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
Grid	💚	$17.25$	$-4.32$	Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
GridPrediction	💚	$138.55$	$-4.87$	GridPrediction_works_as_expected_for_Survival_models
JointModelSamples	💚	$32.29$	$-1.47$	print_works_as_expected_for_JointModelSamples
LongitudinalClaretBruno	💔	$3.24$	$+1.19$	LongitudinalClaretBruno_works_as_expected_with_default_arguments
LongitudinalClaretBruno	👶		$+0.01$	Quantity_models_pass_the_parser
LongitudinalGSF	💔	$2.12$	$+1.47$	LongitudinalGSF_works_as_expected_with_default_arguments
LongitudinalGSF	👶		$+0.02$	Quantity_models_pass_the_parser
LongitudinalQuantiles	💚	$49.51$	$-1.97$	Test_that_LongitudinalQuantities_works_as_expected
LongitudinalRandomSlope	💔	$15.26$	$+3.74$	Print_method_for_LongitudinalRandomSlope_works_as_expected
LongitudinalRandomSlope	👶		$+0.00$	Quantity_models_pass_the_parser
LongitudinalSteinFojo	👶		$+0.03$	Quantity_models_pass_the_parser
SurvivalLoglogistic	💚	$9.53$	$-4.49$	sim_os_loglogistic_is_consistant_with_flexsurv
SurvivalQuantities	💔	$24.48$	$+5.64$	SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
brierScore	💔	$3.84$	$+1.83$	brierScore_SurvivalQuantities_returns_same_results_as_survreg
compile	💚	$6.56$	$-5.45$	compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
extract_quantities	💔	$0.87$	$+2.38$	extract_quantities_works_as_expected
model_multi_chain	💚	$7.88$	$-2.29$	Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
stan_functions	💔	$25.55$	$+1.17$	GSF_SLD_function_works_as_expected

Results for commit 8581191

♻️ This comment has been updated with latest results.