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Fix generating quantities not using correct max value #306

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merged 3 commits into from
Apr 11, 2024

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@gowerc gowerc commented Apr 10, 2024

Closes #305

Issue was code incorrectly always looked for last tumour time rather than last event time when generating survival quantities

@gowerc gowerc requested review from danielinteractive and removed request for danielinteractive April 10, 2024 16:36
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gowerc commented Apr 10, 2024

actually consider this as draft just noticed some small things I need to clean up

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github-actions bot commented Apr 10, 2024

Unit Tests Summary

  1 files   41 suites   7m 36s ⏱️
125 tests  94 ✅ 31 💤 0 ❌
877 runs  846 ✅ 31 💤 0 ❌

Results for commit 3ae4c58.

♻️ This comment has been updated with latest results.

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github-actions bot commented Apr 10, 2024

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
Grid 💚 $104.74$ $-2.03$ $+4$ $0$ $0$ $0$
LongitudinalRandomSlope 💔 $46.95$ $+1.92$ $0$ $0$ $0$ $0$
SurvivalLoglogistic 💔 $29.45$ $+1.53$ $0$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
Grid 💚 $104.47$ $-2.02$ GridObservered_Constructs_correct_quantities
Grid 👶 $+0.02$ coalesceGridTime_works_as_expected
LongitudinalRandomSlope 💔 $29.17$ $+1.15$ LongitudinalRandomSlope_correctly_generates_an_intercept_per_study
SurvivalLoglogistic 💔 $29.29$ $+1.53$ SurvivalLogLogistic_can_recover_known_values
utilities 💀 $0.03$ $-0.03$ expand_time_grid_works_as_expected
utilities 👶 $+0.03$ validate_time_grid_works_as_expected

Results for commit 6f3f7d0

♻️ This comment has been updated with latest results.

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gowerc commented Apr 10, 2024

Ok i think this should be ready now

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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                      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                         27       1  96.30%   51
R/Grid.R                             30       0  100.00%
R/GridEven.R                         32       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/JointModel.R                      122       8  93.44%   142-144, 194, 198, 240, 286, 292
R/JointModelSamples.R                65       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                37      12  67.57%   70-85
R/LongitudinalQuantities.R           67       0  100.00%
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                       60       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               51       0  100.00%
R/SimLongitudinalRandomSlope.R       42       0  100.00%
R/SimLongitudinalSteinFojo.R         48       0  100.00%
R/SimSurvival.R                     104       0  100.00%
R/StanModel.R                        15       0  100.00%
R/StanModule.R                      179       6  96.65%   199-200, 242, 253, 390, 418
R/SurvivalExponential.R              10       0  100.00%
R/SurvivalLoglogistic.R              11       0  100.00%
R/SurvivalModel.R                    19       0  100.00%
R/SurvivalQuantities.R              166       1  99.40%   128
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                              2545     108  95.76%

Diff against main

Filename                      Stmts    Miss  Cover
--------------------------  -------  ------  --------
R/generics.R                     +2       0  +0.30%
R/GridFixed.R                    +6       0  +100.00%
R/GridGrouped.R                  +6       0  +100.00%
R/LongitudinalQuantities.R       +6       0  +100.00%
R/SurvivalQuantities.R           +6       0  +0.02%
R/utilities.R                    -3       0  -0.01%
TOTAL                           +23       0  +0.04%

Results for commit: 3ae4c58

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

@gowerc gowerc merged commit a273133 into main Apr 11, 2024
22 checks passed
@gowerc gowerc deleted the fix/survival-only-quantities branch April 11, 2024 11:27
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Generating survival only quantities results in an error due to missing tumour times
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