451: Support for different priors

[danielinteractive]

closes #451

For the survival models, we can set different independent normal priors for the coefficients of the covariates in the linear predictor using the prior_normal_vector() specification. Here we can give a vector of the same length as the number of design matrix columns for both the means or standard deviations of the normal distributions, or we can give a single value that will be repeated for all covariates.
For example, say we have 3 design matrix columns, i.e. coefficients, in the linear predictor of the survival model, then we can set the priors for these coefficients as follows:

survival_model <- SurvivalWeibullPH(
    beta = prior_normal_vector(mus = c(-1, 0, 5), sigmas = c(1, 1, 10))
)
survival_model

You can run

head(model.matrix(object@survival))

on a DataJoint object to know the columns of the design matrix and then match the positions. This is kind of a workaround but is already practical to use now. More sophisticated solution might come from #11

To do:

• Explain current workaround for finding out the design matrix columns

[github-actions]

Unit Tests Summary

    1 files    195 suites   7m 38s ⏱️
  173 tests   158 ✅ 15 💤 0 ❌
1 147 runs  1 130 ✅ 17 💤 0 ❌

Results for commit a74af59.

♻️ 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	💔	$1.78$	$+62.62$	$0$	$0$	$0$	$0$
compile	💔	$5.39$	$+1.47$	$0$	$0$	$0$	$0$
misc_models	💔	$7.59$	$+1.59$	$0$	$0$	$0$	$0$
model_multi_chain	💔	$7.22$	$+6.58$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
DataSurvival	👶		$+0.00$	model.matrix_for_DataSurvival_works_as_expected
Grid	💔	$39.22$	$+10.64$	Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
GridPrediction	💔	$97.52$	$+27.81$	GridPrediction_works_as_expected_for_Survival_models
JointModelSamples	💔	$28.78$	$+9.29$	print_works_as_expected_for_JointModelSamples
LongitudinalClaretBruno	💔	$5.03$	$+2.17$	LongitudinalClaretBruno_works_as_expected_with_default_arguments
LongitudinalGSF	💔	$5.77$	$+1.68$	LongitudinalGSF_works_as_expected_with_default_arguments
LongitudinalQuantiles	💔	$3.30$	$+3.30$	Test_that_LongitudinalQuantities_works_as_expected
LongitudinalRandomEffects	💔	$1.78$	$+62.62$	LongitudinalRandomEffects_works_as_expected
LongitudinalRandomSlope	💚	$50.72$	$-45.21$	Print_method_for_LongitudinalRandomSlope_works_as_expected
Prior	👶		$+0.00$	prior_normal_vector_works_as_expected
SimJointData	💚	$1.09$	$-1.02$	SimJointData_works_as_expected
SurvivalExponential	👶		$+0.00$	Different_priors_for_the_beta_components_are_possible
SurvivalQuantities	💔	$47.07$	$+16.24$	SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
compile	💔	$5.39$	$+1.47$	compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
initialValues	👶		$+0.00$	initialValues_works_also_for_vectorized_parameters
initialValues	👶		$+0.50$	initial_values_for_fixed_distributions_gives_valid_values
initialValues	💀	$0.39$	$-0.39$	intial_values_for_fixed_distributions_gives_valid_values
misc_models	💔	$7.59$	$+1.59$	Longitudinal_Model_doesn_t_print_sampler_rejection_messages
model_multi_chain	💔	$7.22$	$+6.58$	Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
populationHR	💀	$0.01$	$-0.01$	populationHR_works_as_expected_for_alternative_specfications
populationHR	👶		$+0.00$	populationHR_works_as_expected_for_alternative_specifications
populationHR	💔	$15.91$	$+1.63$	populationHR_works_as_expected_for_default_parameters
stan_functions	💔	$11.90$	$+1.01$	GSF_SLD_function_works_as_expected

Results for commit c5d3e12

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                           Stmts    Miss  Cover    Missing
-------------------------------  -------  ------  -------  ------------------------------
R/brier_score.R                      173       1  99.42%   272
R/DataJoint.R                         78       0  100.00%
R/DataLongitudinal.R                 126       1  99.21%   251
R/DataSubject.R                       85       1  98.82%   144
R/DataSurvival.R                     103       0  100.00%
R/defaults.R                          13       9  30.77%   17-59, 86
R/generics.R                          36       5  86.11%   53, 391, 412, 475, 493
R/Grid.R                              27       1  96.30%   183
R/GridEven.R                          36       0  100.00%
R/GridEvent.R                         22       0  100.00%
R/GridFixed.R                         30       0  100.00%
R/GridGrouped.R                       54       0  100.00%
R/GridManual.R                        23       3  86.96%   79-81
R/GridObserved.R                      24       0  100.00%
R/GridPopulation.R                    37       4  89.19%   66, 74-76
R/GridPrediction.R                    37       6  83.78%   85, 93-97
R/JointModel.R                       131       9  93.13%   148-153, 203, 207, 252, 325
R/JointModelSamples.R                 81       0  100.00%
R/link_generics.R                     39      16  58.97%   67-70, 93-96, 115-118, 141-144
R/Link.R                              66       4  93.94%   202-205
R/LinkComponent.R                     24       3  87.50%   92, 121-122
R/LongitudinalClaretBruno.R          123       6  95.12%   221-225, 244
R/LongitudinalGSF.R                  138       0  100.00%
R/LongitudinalModel.R                 29       2  93.10%   68, 70
R/LongitudinalQuantities.R            74       0  100.00%
R/LongitudinalRandomEffects.R         65      17  73.85%   86-111
R/LongitudinalRandomSlope.R           62       6  90.32%   139-143, 156
R/LongitudinalSteinFojo.R            117      10  91.45%   204-208, 247-251
R/Parameter.R                         14       0  100.00%
R/ParameterList.R                     42       1  97.62%   188
R/populationHR.R                      63       0  100.00%
R/Prior.R                            345       8  97.68%   313, 345, 693, 847-861
R/Promise.R                           29       0  100.00%
R/Quantities.R                        61       0  100.00%
R/QuantityGeneratorPopulation.R       23       0  100.00%
R/QuantityGeneratorPrediction.R       48       0  100.00%
R/QuantityGeneratorSubject.R          21       0  100.00%
R/settings.R                          14      14  0.00%    62-78
R/SimGroup.R                           5       0  100.00%
R/SimJointData.R                     180      10  94.44%   133, 302-310
R/SimLongitudinal.R                    5       2  60.00%   22, 41
R/SimLongitudinalClaretBruno.R       107       0  100.00%
R/SimLongitudinalGSF.R               107       0  100.00%
R/SimLongitudinalRandomSlope.R        55       0  100.00%
R/SimLongitudinalSteinFojo.R          77       0  100.00%
R/SimSurvival.R                      165       0  100.00%
R/simulate.R                         364     364  0.00%    47-551
R/StanModel.R                         16       0  100.00%
R/StanModule.R                       186       6  96.77%   202-203, 247, 258, 409, 437
R/SurvivalExponential.R               14       0  100.00%
R/SurvivalGamma.R                     17       0  100.00%
R/SurvivalLoglogistic.R               15       0  100.00%
R/SurvivalModel.R                     20       0  100.00%
R/SurvivalQuantities.R               172       1  99.42%   127
R/SurvivalWeibullPH.R                 25       0  100.00%
R/utilities.R                        149       2  98.66%   15, 351
R/zzz.R                               31      28  9.68%    3-7, 9-32, 39-48
TOTAL                               4223     540  87.21%

Diff against main

Filename                          Stmts    Miss  Cover
------------------------------  -------  ------  --------
R/DataSurvival.R                     +2       0  +100.00%
R/LongitudinalClaretBruno.R          +1       0  +0.04%
R/LongitudinalGSF.R                  +1       0  +100.00%
R/LongitudinalModel.R                +9      +2  -6.90%
R/LongitudinalRandomSlope.R          +2       0  +0.32%
R/LongitudinalSteinFojo.R            +1       0  +0.07%
R/Prior.R                           +66      +2  -0.17%
R/settings.R                         +2      +2  +100.00%
R/SimLongitudinalRandomSlope.R       +5       0  +100.00%
TOTAL                               +89      +6  +0.13%

Results for commit: 7b0d59d

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results