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Simulation function supports multiple studies #278

Merged
merged 4 commits into from
Mar 4, 2024
Merged

Simulation function supports multiple studies #278

merged 4 commits into from
Mar 4, 2024

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gowerc
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@gowerc gowerc commented Mar 1, 2024

Closes #113

Apologies lots of files ended up being edited but I promise its not as bad as it looks! Its more just a symptom that I changed the api for simulate_joint_data() and that function is unfortunately used everywhere.

I opted to making it a bit more explicit so that users now have to explicitly define groups and state which arm/study those groups belong to e.g.

    design = list(
        SimGroup(n = 50, study = "Study-1", arm = "Arm-A"),
        SimGroup(n = 50, study = "Study-1", arm = "Arm-B")
    )

The vast majority of the file changes are me then changing all the calls to meet this pattern.

Given this change I decided to update the RandomSlope model to have a separate intercept term per "study". The remainder of the file changes (mostly the Stan file changes) are simply just supporting this.

@gowerc gowerc requested a review from danielinteractive March 1, 2024 16:04
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github-actions bot commented Mar 1, 2024 •
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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%   245
R/DataSubject.R                   69       1  98.55%   124
R/DataSurvival.R                  77       0  100.00%
R/defaults.R                      10       6  40.00%   18-57, 84
R/generics.R                      19       1  94.74%   49
R/JointModel.R                   122       8  93.44%   142-144, 194, 198, 240, 286, 292
R/JointModelSamples.R             54       0  100.00%
R/Link.R                          55       4  92.73%   159-162
R/LinkComponent.R                 47       5  89.36%   100, 118, 132-149
R/LongitudinalGSF.R               64       0  100.00%
R/LongitudinalModel.R             35      12  65.71%   68-83
R/LongitudinalQuantities.R        85       8  90.59%   100-107
R/LongitudinalRandomSlope.R       27       0  100.00%
R/LongitudinalSteinFojo.R         57       8  85.96%   113-135
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                      12      12  0.00%    55-69
R/simulations_gsf.R               43       0  100.00%
R/simulations_os.R                11       0  100.00%
R/simulations_rs.R                29       0  100.00%
R/simulations_sf.R                40      40  0.00%    17-109
R/simulations.R                  112       0  100.00%
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                           2267     132  94.18%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  --------
R/simulations_gsf.R       +2       0  +100.00%
R/simulations_rs.R        +8       0  +100.00%
R/simulations_sf.R        +2      +2  +100.00%
R/simulations.R          +11       0  +100.00%
TOTAL                    +23      +2  -0.03%

Results for commit: e95d411

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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Unit Tests Summary

  1 files   36 suites   5m 14s ⏱️
113 tests  87 ✅ 26 💤 0 ❌
810 runs  784 ✅ 26 💤 0 ❌

Results for commit e95d411.

♻️ This comment has been updated with latest results.

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github-actions bot commented Mar 1, 2024 •
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Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
LongitudinalRandomSlope 💔 $0.07$ $+24.31$ $+1$ $0$ $0$ $0$
misc_models 💚 $21.08$ $-20.21$ $0$ $0$ $0$ $0$
model_random_slope_2chain 💔 $37.19$ $+1.82$ $0$ $0$ $0$ $0$
stan_functions 💔 $46.57$ $+2.48$ $0$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
LongitudinalRandomSlope 👶 $+24.31$ LongitudinalRandomSlope_correctly_generates_an_intercept_per_study
misc_models 💚 $21.08$ $-20.21$ Longitudinal_Model_doesn_t_print_sampler_rejection_messages
model_random_slope_2chain 💔 $37.19$ $+1.82$ Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
simulations 👶 $+0.03$ SimGroup_works_as_expected
simulations 👶 $+0.29$ simulate_joint_data_correctly_generates_an_intercept_per_study

Results for commit 2ffbcae

♻️ This comment has been updated with latest results.

danielinteractive
danielinteractive reviewed Mar 3, 2024
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@gowerc gowerc merged commit 6cafea7 into main Mar 4, 2024
23 checks passed
@gowerc gowerc deleted the feature/sim-studies branch March 4, 2024 13:54
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@danielinteractive danielinteractive danielinteractive approved these changes

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Update simulation function to support multiple studies
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@gowerc @danielinteractive