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Add documentation for missing survival distributions #297

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merged 2 commits into from
Apr 2, 2024

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gowerc
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@gowerc gowerc commented Mar 28, 2024

Closes #279

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github-actions bot commented Mar 28, 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                         23       1  95.65%   49
R/JointModel.R                      122       8  93.44%   142-144, 194, 198, 240, 286, 292
R/JointModelSamples.R                55       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           85       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                      105       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              155       6  96.13%   178-183
R/SurvivalWeibullPH.R                11       0  100.00%
R/utilities.R                       146       1  99.32%   13
R/zzz.R                              28      25  10.71%   3, 8-12, 14-35, 47
TOTAL                              2399     110  95.41%

Diff against main

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

Results for commit: c283c9a

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented Mar 28, 2024

Unit Tests Summary

  1 files   40 suites   5m 47s ⏱️
122 tests  91 ✅ 31 💤 0 ❌
853 runs  822 ✅ 31 💤 0 ❌

Results for commit c283c9a.

♻️ This comment has been updated with latest results.

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github-actions bot commented Mar 28, 2024

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
LongitudinalGSF 💚 $227.87$ $-226.63$ $-5$ $+1$ $0$ $0$
LongitudinalSteinFojo 💚 $285.75$ $-284.59$ $-5$ $+1$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
LongitudinalGSF 💚 $226.63$ $-226.63$ Can_recover_known_distributional_parameters_from_a_full_GSF_joint_model
LongitudinalSteinFojo 💚 $284.60$ $-284.59$ Can_recover_known_distributional_parameters_from_a_SF_joint_model

Results for commit c27d84b

♻️ This comment has been updated with latest results.

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Thanks @gowerc, please see below, e.g. some "rate" vs. "scale" points

vignettes/statistical-specification.Rmd Outdated Show resolved Hide resolved
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vignettes/statistical-specification.Rmd Show resolved Hide resolved
@gowerc gowerc merged commit 502463d into main Apr 2, 2024
22 checks passed
@gowerc gowerc deleted the docs/add-missing-survival branch April 2, 2024 19:59
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Documentation: Add missing survival distributions
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