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Convert "patient" -> "subject" #331

Merged
merged 3 commits into from
May 22, 2024
Merged

Convert "patient" -> "subject" #331

merged 3 commits into from
May 22, 2024

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gowerc
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@gowerc gowerc commented May 22, 2024

Closes #325 and #216

Basically a mass find and replace of pt / patient -> subject. Had to go through it all manually as there was a lot of "excePT" and "intercePT" which made a literal find and replace unviable :(

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github-actions bot commented May 22, 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%   244
R/DataSubject.R                       85       1  98.82%   142
R/DataSurvival.R                      98       0  100.00%
R/defaults.R                          10       6  40.00%   18-57, 84
R/generics.R                          31       4  87.10%   51, 395, 414, 449
R/Grid.R                              27       1  96.30%   170
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/GridPopulation.R                    31       4  87.10%   61, 69-71
R/GridPrediction.R                    36       6  83.33%   83, 91-95
R/JointModel.R                       123       8  93.50%   141-143, 193, 197, 239, 285, 291
R/JointModelSamples.R                 59       0  100.00%
R/link_generics.R                     13       3  76.92%   59, 76, 91
R/Link.R                              62       4  93.55%   200-203
R/LinkComponent.R                     19       3  84.21%   88, 120-121
R/LongitudinalGSF.R                   82       0  100.00%
R/LongitudinalModel.R                 19       0  100.00%
R/LongitudinalQuantities.R            71       0  100.00%
R/LongitudinalRandomSlope.R           41       5  87.80%   93-97
R/LongitudinalSteinFojo.R             75       5  93.33%   143-147
R/Parameter.R                         14       0  100.00%
R/ParameterList.R                     42       1  97.62%   184
R/Prior.R                            236       8  96.61%   481, 577, 589-607
R/Promise.R                           25       0  100.00%
R/Quantities.R                        60       0  100.00%
R/QuantityGeneratorPopulation.R       22       0  100.00%
R/QuantityGeneratorPrediction.R       48       0  100.00%
R/QuantityGeneratorSubject.R          19       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                53       0  100.00%
R/SimLongitudinalRandomSlope.R        42       0  100.00%
R/SimLongitudinalSteinFojo.R          50       0  100.00%
R/SimSurvival.R                      104       0  100.00%
R/StanModel.R                         15       0  100.00%
R/StanModule.R                       176       6  96.59%   192-193, 235, 246, 383, 411
R/SurvivalExponential.R               10       0  100.00%
R/SurvivalLoglogistic.R               11       0  100.00%
R/SurvivalModel.R                     19       0  100.00%
R/SurvivalQuantities.R               170       1  99.41%   125
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                               2792     113  95.95%

Diff against main

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

Results for commit: 9a01210

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

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github-actions bot commented May 22, 2024

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
DataJoint 💚 $1.43$ $-1.43$ $-35$ $0$ $0$ $0$
Grid 💚 $231.18$ $-231.18$ $-40$ $0$ $0$ $0$
GridPrediction 💚 $144.11$ $-144.10$ $-13$ $0$ $0$ $0$
Link 💚 $1.42$ $-1.42$ $-8$ $0$ $0$ $0$
LinkComponent 💚 $2.97$ $-2.95$ $-17$ $-1$ $0$ $0$
LongitudinalGSF 💚 $1.98$ $-1.97$ $-9$ $-1$ $0$ $0$
LongitudinalQuantiles 💚 $14.01$ $-14.01$ $-27$ $-1$ $0$ $0$
LongitudinalRandomSlope 💚 $25.36$ $-25.36$ $-4$ $-1$ $0$ $0$
LongitudinalSteinFojo 💚 $2.79$ $-2.78$ $-16$ $-2$ $0$ $0$
SimSurvival 💚 $2.84$ $-2.84$ $-4$ $0$ $0$ $0$
SurvivalExponential 💚 $6.50$ $-6.50$ $-1$ $0$ $0$ $0$
SurvivalLoglogistic 💚 $5.89$ $-5.89$ $-2$ $0$ $0$ $0$
SurvivalQuantities 💚 $52.19$ $-52.17$ $-32$ $-1$ $0$ $0$
SurvivalWeibullPH 💚 $7.19$ $-7.17$ $-1$ $-1$ $0$ $0$
brierScore 💚 $2.44$ $-2.44$ $-3$ $0$ $0$ $0$
compile 💚 $15.79$ $-15.55$ $0$ $0$ $0$ $0$
initialValues 💚 $1.75$ $-1.25$ $-14$ $0$ $0$ $0$
model_multi_chain 💔 $11.38$ $+34.82$ $0$ $0$ $0$ $0$
stan_functions 💚 $1.39$ $-1.39$ $-3$ $0$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
DataJoint 💀 $1.13$ $-1.13$ DataJoint_basic_usage
DataJoint 💀 $0.05$ $-0.05$ DataJoint_errors_if_inconsistent_subject_IDs
DataJoint 💀 $0.15$ $-0.15$ DataJoint_print_method_works_as_expected
DataJoint 💀 $0.02$ $-0.02$ DataJoint_sorts_handles_character_to_factor_levels_correctly
DataJoint 💀 $0.03$ $-0.03$ DataJoint_sorts_handles_pre_factored_levels_correctly
DataJoint 💀 $0.01$ $-0.01$ Error_Handling
DataJoint 💀 $0.04$ $-0.04$ subset_DataJoint_works_as_expected
DataJoint 👶 $+0.07$ DataJoint_basic_usage
DataJoint 👶 $+0.01$ DataJoint_errors_if_inconsistent_subject_IDs
DataJoint 👶 $+0.00$ DataJoint_print_method_works_as_expected
DataJoint 👶 $+0.00$ DataJoint_sorts_handles_character_to_factor_levels_correctly
DataJoint 👶 $+0.00$ DataJoint_sorts_handles_pre_factored_levels_correctly
DataJoint 👶 $+0.00$ Error_Handling
DataJoint 👶 $+0.01$ subset_DataJoint_works_as_expected
DataLongitudinal 💀 $0.06$ $-0.06$ DataLongitudinal_being_rendered_to_list_is_as_expected_for_simple_inputs
DataLongitudinal 💀 $0.04$ $-0.04$ DataSurvival_print_method_works_as_expected
DataLongitudinal 👶 $+2.71$ DataLongitudinal_being_rendered_to_list_is_as_expected_for_simple_inputs
DataLongitudinal 👶 $+0.00$ DataSurvival_print_method_works_as_expected
DataSubject 💀 $0.04$ $-0.04$ DataSubject_print_method_works_as_expected
DataSubject 💀 $0.09$ $-0.09$ DataSubject_works_as_expected
DataSubject 👶 $+0.00$ DataSubject_print_method_works_as_expected
DataSubject 👶 $+0.09$ DataSubject_works_as_expected
DataSurvival 💀 $0.06$ $-0.06$ DataSurvival_being_rendered_to_list_is_as_expected_for_simple_inputs
DataSurvival 💀 $0.06$ $-0.06$ DataSurvival_print_method_works_as_expected
DataSurvival 💀 $0.20$ $-0.20$ mirror_design_matrix_works_as_expected
DataSurvival 👶 $+0.32$ DataSurvival_being_rendered_to_list_is_as_expected_for_simple_inputs
DataSurvival 👶 $+0.00$ DataSurvival_print_method_works_as_expected
DataSurvival 👶 $+0.02$ mirror_design_matrix_works_as_expected
Grid 💀 $34.52$ $-34.52$ GridFixed_bug_has_been_fixed
Grid 💀 $87.50$ $-87.50$ GridObservered_Constructs_correct_quantities
Grid 💀 $0.01$ $-0.01$ GridPopulation_doesn_t_work_with_SurvivalQuantities
Grid 💀 $44.36$ $-44.36$ GridPopulation_works_as_expected_for_GSF_models
Grid 💀 $33.75$ $-33.75$ GridPopulation_works_as_expected_for_Longitudinal_models
Grid 💀 $30.99$ $-30.99$ Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
Grid 💀 $0.02$ $-0.02$ coalesceGridTime_works_as_expected
Grid 💀 $0.03$ $-0.03$ subjects_to_list_works_as_expected
Grid 👶 $+0.00$ GridFixed_bug_has_been_fixed
Grid 👶 $+0.01$ GridObservered_Constructs_correct_quantities
Grid 👶 $+0.00$ GridPopulation_doesn_t_work_with_SurvivalQuantities
Grid 👶 $+0.00$ GridPopulation_works_as_expected_for_GSF_models
Grid 👶 $+0.00$ GridPopulation_works_as_expected_for_Longitudinal_models
Grid 👶 $+40.70$ Grid_objects_work_with_QuantityGenerator_and_QuantityCollapser
Grid 👶 $+0.00$ coalesceGridTime_works_as_expected
Grid 👶 $+0.00$ subjects_to_list_works_as_expected
GridPrediction 💀 $0.08$ $-0.08$ GridPrediction_error_handling_works_as_expected
GridPrediction 💀 $0.01$ $-0.01$ GridPrediction_throws_an_error_if_key_column_already_exists
GridPrediction 💀 $116.82$ $-116.82$ GridPrediction_works_as_expected_for_Survival_models
GridPrediction 💀 $26.88$ $-26.88$ GridPrediction_works_for_survival_only_models
GridPrediction 💀 $0.31$ $-0.31$ getPredictionNames_works_as_expected
GridPrediction 👶 $+0.01$ GridPrediction_error_handling_works_as_expected
GridPrediction 👶 $+0.00$ GridPrediction_throws_an_error_if_key_column_already_exists
GridPrediction 👶 $+151.23$ GridPrediction_works_as_expected_for_Survival_models
GridPrediction 👶 $+0.01$ GridPrediction_works_for_survival_only_models
GridPrediction 👶 $+0.01$ getPredictionNames_works_as_expected
JointModel 💀 $0.17$ $-0.17$ JointModel_print_method_works_as_expected
JointModel 💀 $0.52$ $-0.52$ JointModel_smoke_tests
JointModel 👶 $+0.00$ JointModel_print_method_works_as_expected
JointModel 👶 $+0.73$ JointModel_smoke_tests
JointModelSamples 💀 $5.59$ $-5.59$ print_works_as_expected_for_JointModelSamples
JointModelSamples 👶 $+5.63$ print_works_as_expected_for_JointModelSamples
Link 💀 $0.01$ $-0.01$ Link_prints_as_expected
Link 💀 $0.39$ $-0.39$ Link_works_as_expected
Link 💀 $1.01$ $-1.01$ link_none_works_as_expected
Link 👶 $+0.00$ Link_prints_as_expected
Link 👶 $+0.00$ Link_works_as_expected
Link 👶 $+1.24$ link_none_works_as_expected
LinkComponent 💀 $0.05$ $-0.05$ LinkComponents_are_constructed_correctly_and_can_access_key_components
LinkComponent 💀 $0.62$ $-0.62$ Model_specific_links_return_the_correct_stan_code
LinkComponent 💀 $0.06$ $-0.06$ PromiseLinkComponents_work_as_expected
LinkComponent 💀 $0.64$ $-0.64$ all_link_files_pass_stan_s_syntax_checker
LinkComponent 💀 $1.57$ $-1.57$ complete_models_with_links_pass_stan_s_syntax_checker
LinkComponent 💀 $0.02$ $-0.02$ print_works_as_expected
LinkComponent 👶 $+0.01$ LinkComponents_are_constructed_correctly_and_can_access_key_components
LinkComponent 👶 $+0.01$ Model_specific_links_return_the_correct_stan_code
LinkComponent 👶 $+0.02$ PromiseLinkComponents_work_as_expected
LinkComponent 👶 $+2.97$ all_link_files_pass_stan_s_syntax_checker
LinkComponent 👶 $+0.00$ complete_models_with_links_pass_stan_s_syntax_checker
LinkComponent 👶 $+0.00$ print_works_as_expected
LongitudinalGSF 💀 $0.01$ $-0.01$ Can_recover_known_distributional_parameters_from_a_full_GSF_joint_model
LongitudinalGSF 💀 $0.90$ $-0.90$ Centralised_parameterisation_compiles_without_issues
LongitudinalGSF 💀 $0.12$ $-0.12$ LongitudinalGSF_works_as_expected_with_default_arguments
LongitudinalGSF 💀 $0.82$ $-0.82$ Non_Centralised_parameterisation_compiles_without_issues
LongitudinalGSF 💀 $0.13$ $-0.13$ Print_method_for_LongitudinalGSF_works_as_expected
LongitudinalGSF 👶 $+0.00$ Can_recover_known_distributional_parameters_from_a_full_GSF_joint_model
LongitudinalGSF 👶 $+0.02$ Centralised_parameterisation_compiles_without_issues
LongitudinalGSF 👶 $+1.93$ LongitudinalGSF_works_as_expected_with_default_arguments
LongitudinalGSF 👶 $+0.00$ Non_Centralised_parameterisation_compiles_without_issues
LongitudinalGSF 👶 $+0.00$ Print_method_for_LongitudinalGSF_works_as_expected
LongitudinalQuantiles 💀 $2.82$ $-2.82$ LongitudinalQuantities_can_recover_known_results
LongitudinalQuantiles 💀 $2.22$ $-2.22$ LongitudinalQuantities_correctly_subsets_patients_and_rebuilds_correct_value_for_each_sample
LongitudinalQuantiles 💀 $1.26$ $-1.26$ LongitudinalQuantities_print_method_works_as_expected
LongitudinalQuantiles 💀 $4.73$ $-4.73$ Test_that_LongitudinalQuantities_works_as_expected
LongitudinalQuantiles 💀 $2.99$ $-2.99$ autoplot.LongitudinalQuantities_works_as_expected
LongitudinalQuantiles 👶 $+0.01$ LongitudinalQuantities_can_recover_known_results
LongitudinalQuantiles 👶 $+0.00$ LongitudinalQuantities_correctly_subsets_subjects_and_rebuilds_correct_value_for_each_sample
LongitudinalQuantiles 👶 $+0.00$ LongitudinalQuantities_print_method_works_as_expected
LongitudinalQuantiles 👶 $+43.56$ Test_that_LongitudinalQuantities_works_as_expected
LongitudinalQuantiles 👶 $+0.01$ autoplot.LongitudinalQuantities_works_as_expected
LongitudinalRandomSlope 💀 $7.45$ $-7.45$ LongitudinalRandomSlope_correctly_generates_an_intercept_per_study
LongitudinalRandomSlope 💀 $0.11$ $-0.11$ Print_method_for_LongitudinalRandomSlope_works_as_expected
LongitudinalRandomSlope 💀 $8.00$ $-8.00$ Random_Slope_Model_can_recover_known_parameter_values
LongitudinalRandomSlope 💀 $9.80$ $-9.80$ Random_Slope_Model_left_censoring_works_as_expected
LongitudinalRandomSlope 👶 $+0.01$ LongitudinalRandomSlope_correctly_generates_an_intercept_per_study
LongitudinalRandomSlope 👶 $+0.55$ Print_method_for_LongitudinalRandomSlope_works_as_expected
LongitudinalRandomSlope 👶 $+0.00$ Random_Slope_Model_can_recover_known_parameter_values
LongitudinalRandomSlope 👶 $+0.00$ Random_Slope_Model_left_censoring_works_as_expected
LongitudinalSteinFojo 💀 $0.01$ $-0.01$ Can_recover_known_distributional_parameters_from_a_SF_joint_model
LongitudinalSteinFojo 💀 $0.02$ $-0.02$ Can_recover_known_distributional_parameters_from_a_SF_joint_model_with_growth_link
LongitudinalSteinFojo 💀 $1.32$ $-1.32$ Centralised_parameterisation_compiles_without_issues
LongitudinalSteinFojo 💀 $0.12$ $-0.12$ LongitudinalSteinFojo_works_as_expected_with_default_arguments
LongitudinalSteinFojo 💀 $1.21$ $-1.21$ Non_Centralised_parameterisation_compiles_without_issues
LongitudinalSteinFojo 💀 $0.12$ $-0.12$ Print_method_for_LongitudinalSteinFojo_works_as_expected
LongitudinalSteinFojo 👶 $+0.00$ Can_recover_known_distributional_parameters_from_a_SF_joint_model
LongitudinalSteinFojo 👶 $+0.01$ Can_recover_known_distributional_parameters_from_a_SF_joint_model_with_growth_link
LongitudinalSteinFojo 👶 $+0.01$ Centralised_parameterisation_compiles_without_issues
LongitudinalSteinFojo 👶 $+2.83$ LongitudinalSteinFojo_works_as_expected_with_default_arguments
LongitudinalSteinFojo 👶 $+0.00$ Non_Centralised_parameterisation_compiles_without_issues
LongitudinalSteinFojo 👶 $+0.00$ Print_method_for_LongitudinalSteinFojo_works_as_expected
Parameter 💀 $0.03$ $-0.03$ Parameters_smoke_tests
Parameter 💀 $0.01$ $-0.01$ show_works_for_Paramneter_objects
Parameter 👶 $+0.09$ Parameters_smoke_tests
Parameter 👶 $+0.00$ show_works_for_Paramneter_objects
ParameterList 💀 $0.05$ $-0.05$ ParameterList_smoke_tests
ParameterList 💀 $0.03$ $-0.03$ show_works_for_ParameterList_objects
ParameterList 👶 $+0.12$ ParameterList_smoke_tests
ParameterList 👶 $+0.00$ show_works_for_ParameterList_objects
Prior 💀 $0.12$ $-0.12$ Invalid_prior_parameters_are_rejected
Prior 💀 $0.18$ $-0.18$ Priors_work_as_expected
Prior 💀 $0.03$ $-0.03$ jmpost.prior_shrinkage_works_as_expected
Prior 💀 $0.01$ $-0.01$ show_works_for_Prior_objects
Prior 👶 $+0.01$ Invalid_prior_parameters_are_rejected
Prior 👶 $+0.41$ Priors_work_as_expected
Prior 👶 $+0.02$ jmpost.prior_shrinkage_works_as_expected
Prior 👶 $+0.00$ show_works_for_Prior_objects
Quantities 💀 $0.03$ $-0.03$ Quantities_print_method_works_as_expected
Quantities 💀 $0.02$ $-0.02$ Simple_utility_functions_work_as_expected
Quantities 💀 $0.01$ $-0.01$ as.data.frame.Quantiles_works_as_expected
Quantities 💀 $0.03$ $-0.03$ collapse_quantities_works_as_expected
Quantities 💀 $0.01$ $-0.01$ summary.Quantiles_works_as_expected
Quantities 👶 $+0.00$ Quantities_print_method_works_as_expected
Quantities 👶 $+0.16$ Simple_utility_functions_work_as_expected
Quantities 👶 $+0.00$ as.data.frame.Quantiles_works_as_expected
Quantities 👶 $+0.01$ collapse_quantities_works_as_expected
Quantities 👶 $+0.00$ summary.Quantiles_works_as_expected
SimGroup 💀 $0.05$ $-0.05$ SimGroup_works_as_expected
SimGroup 👶 $+0.12$ SimGroup_works_as_expected
SimJointData 💀 $0.19$ $-0.19$ SimJointData_leads_to_valid_DataJoint_with_almost_only_default_arguments
SimJointData 💀 $0.25$ $-0.25$ SimJointData_works_as_expected
SimJointData 💀 $0.46$ $-0.46$ print_methods_work_as_expected
SimJointData 👶 $+0.00$ SimJointData_leads_to_valid_DataJoint_with_almost_only_default_arguments
SimJointData 👶 $+0.85$ SimJointData_works_as_expected
SimJointData 👶 $+0.00$ print_methods_work_as_expected
SimLongitudinalGSF 💀 $0.09$ $-0.09$ SimLongitudinalGSF_works_as_expected
SimLongitudinalGSF 💀 $0.01$ $-0.01$ print_methods_work_as_expected
SimLongitudinalGSF 👶 $+0.15$ SimLongitudinalGSF_works_as_expected
SimLongitudinalGSF 👶 $+0.00$ print_methods_work_as_expected
SimLongitudinalRandomSlope 💀 $0.15$ $-0.15$ SimLongitudinalRandomSlope_correctly_generates_a_dataset_with_known_parameters
SimLongitudinalRandomSlope 💀 $0.07$ $-0.07$ SimLongitudinalRandomSlope_works_as_expected
SimLongitudinalRandomSlope 💀 $0.01$ $-0.01$ print_methods_work_as_expected
SimLongitudinalRandomSlope 👶 $+0.00$ SimLongitudinalRandomSlope_correctly_generates_a_dataset_with_known_parameters
SimLongitudinalRandomSlope 👶 $+0.44$ SimLongitudinalRandomSlope_works_as_expected
SimLongitudinalRandomSlope 👶 $+0.00$ print_methods_work_as_expected
SimLongitudinalSteinFojo 💀 $0.08$ $-0.08$ SimLongitudinalSteinFojo_works_as_expected
SimLongitudinalSteinFojo 💀 $0.02$ $-0.02$ print_methods_work_as_expected
SimLongitudinalSteinFojo 👶 $+0.16$ SimLongitudinalSteinFojo_works_as_expected
SimLongitudinalSteinFojo 👶 $+0.00$ print_methods_work_as_expected
SimSurvival 💀 $1.00$ $-1.00$ SimSurvivalExponential_creates_a_dataset_with_the_correct_parameter
SimSurvival 💀 $1.82$ $-1.82$ SimSurvivalWeibullPH_creates_a_dataset_with_the_correct_parameter
SimSurvival 💀 $0.01$ $-0.01$ print_methods_work_as_expected
SimSurvival 👶 $+3.70$ SimSurvivalExponential_creates_a_dataset_with_the_correct_parameter
SimSurvival 👶 $+0.00$ SimSurvivalWeibullPH_creates_a_dataset_with_the_correct_parameter
SimSurvival 👶 $+0.00$ print_methods_work_as_expected
StanModel 💀 $0.03$ $-0.03$ StanModel_print_function_works_as_expected
StanModel 👶 $+0.08$ StanModel_print_function_works_as_expected
StanModule 💀 $0.09$ $-0.09$ StanModule.merge_works_as_expected
StanModule 💀 $0.03$ $-0.03$ StanModule_can_handle_trailing_characters
StanModule 💀 $0.03$ $-0.03$ StanModule_can_load_vignette_example_code
StanModule 💀 $0.04$ $-0.04$ StanModule_can_read_basic_stan_programs
StanModule 💀 $0.03$ $-0.03$ StanModule_print_method_works_as_expected
StanModule 💀 $0.01$ $-0.01$ StanModule_throws_a_warning_if_non_empty_string_generates_empty_object
StanModule 💀 $0.01$ $-0.01$ StanModule_throws_an_error_for_1_line_blocks
StanModule 💀 $0.01$ $-0.01$ StanModule_throws_an_error_for_code_after_the_closing_bracket
StanModule 💀 $0.03$ $-0.03$ StanModule_works_with_in_line_code
StanModule 👶 $+0.01$ StanModule.merge_works_as_expected
StanModule 👶 $+0.01$ StanModule_can_handle_trailing_characters
StanModule 👶 $+0.01$ StanModule_can_load_vignette_example_code
StanModule 👶 $+0.01$ StanModule_can_read_basic_stan_programs
StanModule 👶 $+0.34$ StanModule_print_method_works_as_expected
StanModule 👶 $+0.00$ StanModule_throws_a_warning_if_non_empty_string_generates_empty_object
StanModule 👶 $+0.00$ StanModule_throws_an_error_for_1_line_blocks
StanModule 👶 $+0.00$ StanModule_throws_an_error_for_code_after_the_closing_bracket
StanModule 👶 $+0.01$ StanModule_works_with_in_line_code
SurvivalExponential 💀 $0.09$ $-0.09$ Print_method_for_SurvivalExponential_works_as_expected
SurvivalExponential 💀 $6.41$ $-6.41$ SurvivalExponential_can_recover_true_parameter_including_covariates_
SurvivalExponential 👶 $+0.00$ Print_method_for_SurvivalExponential_works_as_expected
SurvivalExponential 👶 $+27.46$ SurvivalExponential_can_recover_true_parameter_including_covariates_
SurvivalLoglogistic 💀 $0.09$ $-0.09$ Print_method_for_SurvivalLogLogistic_works_as_expected
SurvivalLoglogistic 💀 $5.77$ $-5.77$ SurvivalLogLogistic_can_recover_known_values
SurvivalLoglogistic 💀 $0.02$ $-0.02$ sim_os_loglogistic_is_consistant_with_flexsurv
SurvivalLoglogistic 👶 $+0.00$ Print_method_for_SurvivalLogLogistic_works_as_expected
SurvivalLoglogistic 👶 $+0.00$ SurvivalLogLogistic_can_recover_known_values
SurvivalLoglogistic 👶 $+2.69$ sim_os_loglogistic_is_consistant_with_flexsurv
SurvivalQuantities 💀 $43.45$ $-43.45$ SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
SurvivalQuantities 💀 $1.53$ $-1.53$ SurvivalQuantities_print_method_works_as_expected
SurvivalQuantities 💀 $2.71$ $-2.71$ SurvivalQuantities_works_with_time_0
SurvivalQuantities 💀 $4.50$ $-4.50$ autoplot.SurvivalSamples_works_as_expected
SurvivalQuantities 👶 $+10.64$ SurvivalQuantities_and_autoplot.SurvivalQuantities_works_as_expected
SurvivalQuantities 👶 $+0.00$ SurvivalQuantities_print_method_works_as_expected
SurvivalQuantities 👶 $+0.02$ SurvivalQuantities_works_with_time_0
SurvivalQuantities 👶 $+0.02$ autoplot.SurvivalSamples_works_as_expected
SurvivalWeibullPH 💀 $0.08$ $-0.08$ Print_method_for_SurvivalWeibullPH_works_as_expected
SurvivalWeibullPH 💀 $7.11$ $-7.11$ SurvivalWeibullPH_can_recover_known_values
SurvivalWeibullPH 👶 $+7.65$ Print_method_for_SurvivalWeibullPH_works_as_expected
SurvivalWeibullPH 👶 $+0.01$ SurvivalWeibullPH_can_recover_known_values
brierScore 💀 $2.31$ $-2.31$ brierScore_SurvivalQuantities_returns_same_results_as_survreg
brierScore 💀 $0.01$ $-0.01$ brier_score_weight_matrix_is_correctly_calculated
brierScore 💀 $0.01$ $-0.01$ bs_get_squared_dist_works_as_expected
brierScore 💀 $0.12$ $-0.12$ reverse_km_event_first_and_reverse_km_cen_first_work_as_expected
brierScore 👶 $+33.09$ brierScore_SurvivalQuantities_returns_same_results_as_survreg
brierScore 👶 $+0.00$ brier_score_weight_matrix_is_correctly_calculated
brierScore 👶 $+0.00$ bs_get_squared_dist_works_as_expected
brierScore 👶 $+0.00$ reverse_km_event_first_and_reverse_km_cen_first_work_as_expected
compile 👶 $+0.24$ compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
compile 💀 $15.79$ $-15.79$ compileStanModel_doesn_t_error_if_the_directory_doesn_t_exist
extract_quantities 👶 $+0.36$ extract_quantities_works_as_expected
extract_quantities 💀 $0.34$ $-0.34$ extract_quantities_works_as_expected
initialValues 👶 $+0.01$ ensure_initial_values_works_as_expected
initialValues 👶 $+1.44$ initialValues_works_as_expected
initialValues 👶 $+0.50$ intial_values_for_fixed_distributions_gives_valid_values
initialValues 💀 $0.02$ $-0.02$ ensure_initial_values_works_as_expected
initialValues 💀 $0.19$ $-0.19$ initialValues_works_as_expected
initialValues 💀 $1.54$ $-1.54$ intial_values_for_fixed_distributions_gives_valid_values
jinjar_render 👶 $+0.07$ Basic_Jinjar_syntax_works_with_decorated_render_
jinjar_render 👶 $+0.00$ Global_variables_defined_by_decorated_render_are_usable
jinjar_render 💀 $0.01$ $-0.01$ Basic_Jinjar_syntax_works_with_decorated_render_
jinjar_render 💀 $0.01$ $-0.01$ Global_variables_defined_by_decorated_render_are_usable
longitudinal_plot 👶 $+0.29$ longitudinal_plot_works_as_expected
longitudinal_plot 💀 $0.23$ $-0.23$ longitudinal_plot_works_as_expected
misc_models 👶 $+0.83$ Longitudinal_Model_doesn_t_print_sampler_rejection_messages
misc_models 💀 $0.78$ $-0.78$ Longitudinal_Model_doesn_t_print_sampler_rejection_messages
model_multi_chain 👶 $+46.20$ Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
model_multi_chain 💀 $11.38$ $-11.38$ Can_recover_known_distribution_parameters_from_random_slope_model_when_using_multiple_chains
options 👶 $+0.06$ Can_alter_Gaussian_Quadrature_arguments
options 💀 $0.03$ $-0.03$ Can_alter_Gaussian_Quadrature_arguments
stan_functions 👶 $+0.00$ GSF_Identity_Link_Function_works_as_expected
stan_functions 👶 $+4.12$ GSF_SLD_function_works_as_expected
stan_functions 👶 $+0.00$ Normal_Log_Density_functions_work_as_expected
stan_functions 💀 $0.50$ $-0.50$ GSF_Identity_Link_Function_works_as_expected
stan_functions 💀 $0.44$ $-0.44$ GSF_SLD_function_works_as_expected
stan_functions 💀 $0.46$ $-0.46$ Normal_Log_Density_functions_work_as_expected
survival_plot 👶 $+0.25$ survival_plot_works_as_expected
survival_plot 💀 $0.22$ $-0.22$ survival_plot_works_as_expected
utilities 👶 $+0.00$ add_missing_stan_blocks_works_as_expected
utilities 👶 $+0.00$ decompose_subjects_works_as_expected
utilities 👶 $+0.00$ expand_initial_values_works_as_expected
utilities 👶 $+0.01$ expand_subjects_works_as_expected
utilities 👶 $+0.30$ get_missing_rownumbers_works_as_expected
utilities 👶 $+0.00$ remove_missing_rows_works_as_expected
utilities 👶 $+0.00$ replace_with_lookup_asserts_looked_up_sizes_as_numbers_as_expected
utilities 👶 $+0.00$ replace_with_lookup_asserts_sizes_as_numbers_as_expected
utilities 👶 $+0.00$ replace_with_lookup_works_and_sets_array_attributes_as_expected
utilities 👶 $+0.00$ samples_median_ci_works_as_expected
utilities 👶 $+0.00$ samples_median_ci_works_with_a_custom_credibility_level
utilities 👶 $+0.01$ validate_time_grid_works_as_expected
utilities 💀 $0.01$ $-0.01$ add_missing_stan_blocks_works_as_expected
utilities 💀 $0.04$ $-0.04$ decompose_patients_works_as_expected
utilities 💀 $0.01$ $-0.01$ expand_initial_values_works_as_expected
utilities 💀 $0.03$ $-0.03$ expand_patients_works_as_expected
utilities 💀 $0.03$ $-0.03$ get_missing_rownumbers_works_as_expected
utilities 💀 $0.01$ $-0.01$ remove_missing_rows_works_as_expected
utilities 💀 $0.01$ $-0.01$ replace_with_lookup_asserts_looked_up_sizes_as_numbers_as_expected
utilities 💀 $0.01$ $-0.01$ replace_with_lookup_asserts_sizes_as_numbers_as_expected
utilities 💀 $0.02$ $-0.02$ replace_with_lookup_works_and_sets_array_attributes_as_expected
utilities 💀 $0.01$ $-0.01$ samples_median_ci_works_as_expected
utilities 💀 $0.01$ $-0.01$ samples_median_ci_works_with_a_custom_credibility_level
utilities 💀 $0.04$ $-0.04$ validate_time_grid_works_as_expected

Results for commit 6c03f6a

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Unit Tests Summary

  1 files  140 suites   6m 37s ⏱️
131 tests 104 ✅ 27 💤 0 ❌
929 runs  897 ✅ 32 💤 0 ❌

Results for commit 9a01210.

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super, thanks @gowerc

@gowerc gowerc merged commit 791a0e7 into main May 22, 2024
23 checks passed
@gowerc gowerc deleted the 325-harmoise-subject branch May 22, 2024 10:35
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Replace references to "pt" in the simulation functions to "subject"
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