Fix generating quantities not using correct max value

gowerc commented 7 months ago

Closes #305

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

gowerc commented 7 months ago

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

github-actions[bot] commented 7 months ago

Unit Tests Summary

1 files 41 suites 7m 36s :stopwatch: 125 tests 94 :white_check_mark: 31 :zzz: 0 :x: 877 runs 846 :white_check_mark: 31 :zzz: 0 :x:

Results for commit 3ae4c58f.

:recycle: This comment has been updated with latest results.

github-actions[bot] commented 7 months ago

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 6f3f7d0bad44e0196f154b827378de4ea7b80d31

♻️ This comment has been updated with latest results.

gowerc commented 7 months ago

Ok i think this should be ready now

github-actions[bot] commented 7 months ago

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: 3ae4c58f32e9d45efd1111ea704ce8cdeff9c6d2

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

Genentech / jmpost