Branch for vignettes proposed by FM

[mercifr1]

No description provided.

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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%   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%   51, 395, 415, 470
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                       125       8  93.60%   146-148, 198, 202, 244, 290, 296
R/JointModelSamples.R                 63       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/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       6  92.11%   116, 148-152
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/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                        143       1  99.30%   13
R/zzz.R                               28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                               2825     114  95.96%

Diff against main

Filename                     Stmts    Miss  Cover
-------------------------  -------  ------  --------
R/brier_score.R                 -1       0  +100.00%
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                           -6      -2  +0.08%

Results for commit: 7c44899

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files  140 suites   6m 35s ⏱️
131 tests 128 ✅ 3 💤 0 ❌
978 runs  975 ✅ 3 💤 0 ❌

Results for commit 7c44899.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
LongitudinalClaretBruno	💀	$0.01$	$-0.01$	$-2$	$0$	$0$	$0$
SimLongitudinalClaretBruno	💀	$0.00$	$-0.00$	$-1$	$0$	$0$	$0$
extract_quantities	💚	$3.91$	$-3.61$	$0$	$0$	$0$	$0$
model_multi_chain	💔	$3.96$	$+3.90$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
Grid	💔	$13.90$	$+8.46$	Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
GridPrediction	💔	$126.96$	$+3.05$	GridPrediction_works_as_expected_for_Survival_models
LongitudinalClaretBruno	💀	$0.00$	$-0.00$	Can_recover_known_distributional_parameters_from_a_SF_joint_model
LongitudinalClaretBruno	💀	$0.00$	$-0.00$	Centralised_parameterisation_compiles_without_issues
LongitudinalClaretBruno	💀	$4.33$	$-4.33$	LongitudinalClaretBruno_works_as_expected_with_default_arguments
LongitudinalClaretBruno	💀	$0.01$	$-0.01$	Non_Centralised_parameterisation_compiles_without_issues
LongitudinalClaretBruno	💀	$0.00$	$-0.00$	Print_method_for_LongitudinalClaretBruno_works_as_expected
LongitudinalClaretBruno	💀	$0.01$	$-0.01$	Quantity_models_pass_the_parser
LongitudinalGSF	💚	$3.53$	$-1.50$	LongitudinalGSF_works_as_expected_with_default_arguments
LongitudinalGSF	💀	$0.02$	$-0.02$	Quantity_models_pass_the_parser
LongitudinalRandomSlope	💚	$18.66$	$-4.92$	Print_method_for_LongitudinalRandomSlope_works_as_expected
LongitudinalRandomSlope	💀	$0.00$	$-0.00$	Quantity_models_pass_the_parser
LongitudinalSteinFojo	💚	$4.74$	$-1.83$	LongitudinalSteinFojo_works_as_expected_with_default_arguments
LongitudinalSteinFojo	💀	$0.03$	$-0.03$	Quantity_models_pass_the_parser
SimLongitudinalClaretBruno	💀	$0.20$	$-0.20$	SimLongitudinalClaretBruno_works_as_expected
SimLongitudinalClaretBruno	💀	$0.00$	$-0.00$	print_methods_work_as_expected
SurvivalLoglogistic	💔	$5.28$	$+5.14$	sim_os_loglogistic_is_consistant_with_flexsurv
SurvivalQuantities	💚	$27.26$	$-4.26$	SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
brierScore	💔	$0.58$	$+4.87$	brierScore_SurvivalQuantities_returns_same_results_as_survreg
brierScore	💀	$0.00$	$-0.00$	match_order_works_as_expected
extract_quantities	💚	$3.91$	$-3.61$	extract_quantities_works_as_expected
model_multi_chain	💔	$3.96$	$+3.90$	Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
stan_functions	💚	$26.59$	$-1.16$	GSF_SLD_function_works_as_expected

Results for commit 628fc68

♻️ This comment has been updated with latest results.

[mercifr1]

test