Implement Gamma Survival Model

[gowerc]

Closes #411

Apologies though I have committed the cardinal sin of adding in a few additional unrelated changes that I spotted whilst developing this which include:

• Adding compiler checks for the other survival models
• Converting the other models to only do sampling tests on the CRON job
• Adding parameter lower bounds to the other survival distributions

[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                       126      10  92.06%   146-151, 201, 205, 247, 293, 299
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                               3114     121  96.11%

Diff against main

Filename                 Stmts    Miss  Cover
---------------------  -------  ------  --------
R/SimSurvival.R            +12       0  +100.00%
R/SurvivalGamma.R          +13       0  +100.00%
R/SurvivalWeibullPH.R       +2       0  +100.00%
TOTAL                      +27       0  +0.03%

Results for commit: fbc9f29

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

    1 files    175 suites   5m 58s ⏱️
  153 tests   143 ✅ 10 💤 0 ❌
1 077 runs  1 066 ✅ 11 💤 0 ❌

Results for commit 023f09f.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
SurvivalGamma	👶		$+0.00$	$+1$	$+1$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
Grid	💔	$48.80$	$+1.14$	Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
GridPrediction	💔	$115.36$	$+3.29$	GridPrediction_works_as_expected_for_Survival_models
LongitudinalRandomSlope	💔	$6.27$	$+17.54$	Print_method_for_LongitudinalRandomSlope_works_as_expected
SurvivalExponential	👶		$+2.04$	Can_load_and_compile_SurvivalExponential_model
SurvivalExponential	💚	$22.53$	$-22.53$	SurvivalExponential_can_recover_true_parameter_including_covariates_
SurvivalGamma	👶		$+0.00$	Can_load_and_compile_SurvivalGamma_model
SurvivalGamma	👶		$+2.06$	Print_method_for_SurvivalGamma_works_as_expected
SurvivalGamma	👶		$+0.00$	SimSurvivalGamma_is_consistant_with_flexsurv
SurvivalGamma	👶		$+0.00$	SurvivalGamma_can_recover_known_values
SurvivalLoglogistic	👶		$+1.77$	Can_load_and_compile_SurvivalLogLogistic_model
SurvivalLoglogistic	💚	$18.17$	$-18.17$	sim_os_loglogistic_is_consistant_with_flexsurv
SurvivalWeibullPH	👶		$+0.00$	Can_load_and_compile_SurvivalWeibullPH_model
SurvivalWeibullPH	💚	$8.35$	$-6.96$	Print_method_for_SurvivalWeibullPH_works_as_expected

Results for commit ea0d677

♻️ This comment has been updated with latest results.

[gravesti]

Query on the stan definition of the hazard @gowerc , otherwise looks good!

[gowerc]

Query on the stan definition of the hazard @gowerc , otherwise looks good!

@gravesti - Apologies what do you mean by query on the stan definition? As in does something look wrong to you ?

[gravesti]

@gravesti - Apologies what do you mean by query on the stan definition? As in does something look wrong to you ?

I had another comment but I resolved it. I was confused why the log hazard was defined differently in the stan code. But I found it correct and due to the stan function a normalising term.

[gowerc]

@gravesti - Apologies what do you mean by query on the stan definition? As in does something look wrong to you ?

I had another comment but I resolved it. I was confused why the log hazard was defined differently in the stan code. But I found it correct and due to the stan function a normalising term.

Ah yer apologies I probs should have made a comment to explain that stan automatically adds in the normalising term which isn't done in the R equivalent code.