Added data object documentation

gowerc commented 7 months ago

Closes #280

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%   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: 398b39393f0f6072a841468edcf7a58337add665

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

github-actions[bot] commented 7 months ago

Unit Tests Summary

1 files 40 suites 5m 54s :stopwatch: 122 tests 91 :white_check_mark: 31 :zzz: 0 :x: 853 runs 822 :white_check_mark: 31 :zzz: 0 :x:

Results for commit 398b3939.

: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`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
JointModelSamples	💚	$35.52$	$-3.23$	$0$	$0$	$0$	$0$
LongitudinalQuantiles	💚	$49.39$	$-4.01$	$0$	$0$	$0$	$0$
LongitudinalRandomSlope	💚	$50.09$	$-2.06$	$0$	$0$	$0$	$0$
SurvivalExponential	💚	$30.08$	$-1.79$	$0$	$0$	$0$	$0$
SurvivalLoglogistic	💚	$32.71$	$-3.63$	$0$	$0$	$0$	$0$
SurvivalWeibullPH	💚	$30.81$	$-1.40$	$0$	$0$	$0$	$0$
compile	💚	$15.68$	$-1.56$	$0$	$0$	$0$	$0$
model_multi_chain	💚	$46.80$	$-2.65$	$0$	$0$	$0$	$0$
stan_functions	💚	$52.00$	$-5.78$	$0$	$0$	$0$	$0$

Additional test case details

| Test Suite | $Status$ | Time on `main` | $±Time$ | Test Case | |:-----|:----:|:----:|:----:|:-----| | JointModelSamples | 💚 | $35.52$ | $-3.23$ | print_works_as_expected_for_JointModelSamples | | LongitudinalQuantiles | 💚 | $39.75$ | $-3.84$ | Test_that_LongitudinalQuantities_works_as_expected | | LongitudinalRandomSlope | 💚 | $31.87$ | $-1.86$ | LongitudinalRandomSlope_correctly_generates_an_intercept_per_study | | SurvivalExponential | 💚 | $29.99$ | $-1.79$ | SurvivalExponential_can_recover_true_parameter_including_covariates_ | | SurvivalLoglogistic | 💚 | $32.54$ | $-3.62$ | SurvivalLogLogistic_can_recover_known_values | | SurvivalWeibullPH | 💚 | $30.72$ | $-1.42$ | SurvivalWeibullPH_can_recover_known_values | | compile | 💚 | $15.68$ | $-1.56$ | compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist | | model_multi_chain | 💚 | $46.80$ | $-2.65$ | Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains | | stan_functions | 💚 | $17.74$ | $-2.03$ | GSF_Identity_Link_Function_works_as_expected | | stan_functions | 💚 | $16.87$ | $-1.91$ | GSF_SLD_function_works_as_expected | | stan_functions | 💚 | $17.40$ | $-1.84$ | Normal_Log_Density_functions_work_as_expected |

Results for commit bb753278732fe2f65c14165eb9612d455b729ddc

♻️ This comment has been updated with latest results.

Genentech / jmpost