Different initial values for each mcmc chain

[gowerc]

Closes #4

This ended up being quite a bit more complicated than expected, mostly because the init code was kind of scattered all throughout the program.

I think in particular I would appreciate a double checking of the sample functions as the parameterisations differ in a few cases between Stan and R soo need to double check I'm sampling them correctly.

[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                  74       1  98.65%   146
R/defaults.R                      13       7  46.15%   27, 45-84, 111
R/generics.R                      16       1  93.75%   69
R/JointModel.R                   119       9  92.44%   114-116, 166, 170, 212, 258, 264, 270
R/JointModelSamples.R             54       0  100.00%
R/Link.R                          18       0  100.00%
R/LinkGSF.R                       69      13  81.16%   116-128
R/LinkNone.R                       5       1  80.00%   36
R/LinkRandomSlope.R               11       0  100.00%
R/LongitudinalGSF.R               56       0  100.00%
R/LongitudinalModel.R             17       0  100.00%
R/LongitudinalQuantities.R        85       8  90.59%   100-107
R/LongitudinalRandomSlope.R       20       0  100.00%
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                      11      11  0.00%    40-53
R/simulations_gsf.R               41       0  100.00%
R/simulations_os.R                11       5  54.55%   35-39
R/simulations_rs.R                21       0  100.00%
R/simulations.R                   99       1  98.99%   122
R/StanModel.R                     15       0  100.00%
R/StanModule.R                   177       6  96.61%   199-200, 242, 253, 388, 416
R/SurvivalExponential.R           10       0  100.00%
R/SurvivalLoglogistic.R           11       0  100.00%
R/SurvivalModel.R                 19       0  100.00%
R/SurvivalQuantities.R           151       6  96.03%   173-178
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                           2108      85  95.97%

Diff against main

Filename                       Stmts    Miss  Cover
---------------------------  -------  ------  --------
R/JointModel.R                   +28      +3  -0.97%
R/LongitudinalGSF.R              +16       0  +100.00%
R/LongitudinalRandomSlope.R       -2       0  +100.00%
R/ParameterList.R                 +5       0  +0.32%
R/Prior.R                        +33      +8  -3.39%
R/settings.R                     +11     +11  +100.00%
R/StanModel.R                     +1       0  +100.00%
R/zzz.R                           -9      -9  +100.00%
TOTAL                            +83     +13  -0.48%

Results for commit: 18aaae5

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   35 suites   5m 45s ⏱️
105 tests  80 ✅ 25 💤 0 ❌
780 runs  755 ✅ 25 💤 0 ❌

Results for commit 18aaae5.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
compile	💔	$14.13$	$+1.51$	$0$	$0$	$0$	$0$
initialValues	👶		$+2.13$	$+414$	$0$	$0$	$0$
misc_models	💔	$21.95$	$+2.51$	$0$	$0$	$0$	$0$
stan_functions	💔	$46.97$	$+5.24$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
Prior	👶		$+0.03$	jmpost.prior_shrinkage_works_as_expected
compile	💔	$14.13$	$+1.51$	compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
initialValues	👶		$+0.02$	ensure_initial_values_works_as_expected
initialValues	👶		$+0.52$	initialValues_works_as_expected
initialValues	👶		$+1.59$	intial_values_for_fixed_distributions_gives_valid_values
misc_models	💔	$21.95$	$+2.51$	Longitudinal_Model_doesn_t_print_sampler_rejection_messages
stan_functions	💔	$15.79$	$+2.12$	GSF_Identity_Link_Function_works_as_expected
stan_functions	💔	$15.57$	$+1.46$	GSF_SLD_function_works_as_expected
stan_functions	💔	$15.61$	$+1.66$	Normal_Log_Density_functions_work_as_expected

Results for commit abe9d91

♻️ This comment has been updated with latest results.

[danielinteractive]

Thanks @gowerc ! nice work

[gowerc]

Also now closes #255