Add Stan + jmpost examples

[gowerc]

Closes #250

Attempts to address @mercifr1's request to have a working example showing how jmpost code compares to raw Stan code. Note that jmpost has significantly worse performance due to the fact that we calculate the survival function by approximating the integral of the hazard function (as opposed to the raw Stan code here that just uses the closed form of the survival function as this is an OS only model.)

[danielinteractive]

Thanks @gowerc , looks good, however I wonder if we could directly have this as a vignette in the package itself? As the design folder won't be visible for users, and is just for us as developers?

[gowerc]

Well thats annoying, despite this PR having 0 code changes on the packages code base the automatic roxygen pipeline has decided to re-write all of the help files due to an updated version of the roxygen package 😢

[gowerc]

@danielinteractive - At the moment I was thinking this would just be for us (tbh I'm only including it here as an easy way of sharing with @mercifr1 as opposed to sending an email). I didn't feel vignettes for Stan tutorials was particularly useful for our packages end users as my thinking was that our main purpose was to be to abstract away the raw Stan code?

[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                    91       8  91.21%   113-125, 204, 210, 216
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               24       0  100.00%
R/LongitudinalModel.R             17       0  100.00%
R/LongitudinalQuantities.R        85       8  90.59%   100-107
R/LongitudinalRandomSlope.R       22       0  100.00%
R/Parameter.R                     14       0  100.00%
R/ParameterList.R                 37       1  97.30%   175
R/Prior.R                        117       0  100.00%
R/Quantities.R                   105       0  100.00%
R/simulations_gsf.R               43       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                     14       0  100.00%
R/StanModule.R                   175       6  96.57%   197-198, 240, 251, 386, 414
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                           11      11  0.00%    4-29
TOTAL                           1923      74  96.15%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: 82ba6ce

Minimum allowed coverage is 80%

♻️ 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	💔	$5.47$	$+25.23$	$0$	$0$	$0$	$0$
LongitudinalGSF	💔	$37.86$	$+21.35$	$0$	$0$	$0$	$0$
LongitudinalQuantiles	💔	$13.94$	$+28.01$	$0$	$0$	$0$	$0$
SurvivalExponential	💔	$6.29$	$+22.43$	$0$	$0$	$0$	$0$
brierScore	💔	$5.16$	$+23.43$	$0$	$0$	$0$	$0$
extract_quantities	💔	$0.36$	$+15.00$	$0$	$0$	$0$	$0$
misc_models	💔	$0.83$	$+21.56$	$0$	$0$	$0$	$0$
model_random_slope_2chain	💔	$9.06$	$+26.67$	$0$	$0$	$0$	$0$
stan_functions	💔	$1.27$	$+45.67$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
JointModelSamples	💔	$5.47$	$+25.23$	smoke_test_for_JointModelSamples
LongitudinalGSF	💔	$37.61$	$+21.36$	LongitudinalGSF_works_as_expected_with_a_single_study
LongitudinalQuantiles	💔	$8.15$	$+28.15$	Test_that_LongitudinalQuantities_works_as_expected
SurvivalExponential	💔	$2.84$	$+22.43$	SurvivalExponential_can_recover_true_parameter_no_covariates_
brierScore	💔	$5.02$	$+23.44$	brierScore_SurvivalQuantities_returns_same_results_as_survreg
extract_quantities	💔	$0.36$	$+15.00$	extract_quantities_works_as_expected
misc_models	💔	$0.83$	$+21.56$	Longitudinal_Model_doesn_t_print_sampler_rejection_messages
model_random_slope_2chain	💔	$9.06$	$+26.67$	Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
stan_functions	💔	$0.46$	$+15.73$	GSF_Identity_Link_Function_works_as_expected
stan_functions	💔	$0.38$	$+14.86$	GSF_SLD_function_works_as_expected
stan_functions	💔	$0.44$	$+15.08$	Normal_Log_Density_functions_work_as_expected

Results for commit 422156f

♻️ This comment has been updated with latest results.

[danielinteractive]

I think it could be helpful for Stan users to see the analogies. But ok can keep in design for now

[mercifr1]

Thank you so much!

[mercifr1]

Thanks for putting this together.
Sorry if I am not using the 'review' feature correcting here - I am using it for the 1st time
May I ask what is 'x' and why is it a vector of length 50?

[gowerc]

Good question....

I think this was just some old code that I forgot to delete, as far as I can see x isn't used anywhere in the stan program so it is contributing nothing.

Will clean up in a future update as this PR has already been merged