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Genentech / psborrow2

psborrow2: Bayesian Dynamic Borrowing Simulation Study and Analysis
https://genentech.github.io/psborrow2/
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update psborrow to psborrow2 #208

Closed mattsecrest closed 1 year ago

mattsecrest commented 1 year ago

Pull Request

github-actions[bot] commented 1 year ago

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Code Coverage Summary

Filename                               Stmts    Miss  Cover    Missing
-----------------------------------  -------  ------  -------  -----------------
R/add_covariates.R                        10       0  100.00%
R/analysis_class.R                        41       4  90.24%   90-93
R/bernoulli_prior.R                       16       0  100.00%
R/beta_prior.R                            16       0  100.00%
R/borrowing_class.R                        6       5  16.67%   49-53
R/borrowing_details.R                     14       1  92.86%   88
R/cauchy_prior.R                          16       1  93.75%   69
R/check_data_matrix_has_columns.R         16       0  100.00%
R/cmdstan.R                                6       0  100.00%
R/covariate_class.R                       11      10  9.09%    57-66
R/create_analysis_obj.R                   55       3  94.55%   88-90
R/create_data_matrix.R                    24       0  100.00%
R/create_simulation_obj.R                 63       0  100.00%
R/exp_surv_dist.R                         28       0  100.00%
R/exponential_prior.R                     16       0  100.00%
R/gamma_prior.R                           16       0  100.00%
R/generics.R                               5       3  40.00%   63-87
R/helpers.R                               89       2  97.75%   24, 58
R/logistic_bin_outcome.R                  20       0  100.00%
R/make_analysis_object_list.R             28       0  100.00%
R/make_model_string_data.R                19       0  100.00%
R/make_model_string_functions.R            4       0  100.00%
R/make_model_string_model.R               56       2  96.43%   48, 85
R/make_model_string_parameters.R          21       0  100.00%
R/make_model_string_transf_params.R       10       1  90.00%   29
R/mcmc_sample.R                           98      87  11.22%   73-304
R/mcmc_simulation_result.R                 7       7  0.00%    33-57
R/normal_prior.R                          16       1  93.75%   69
R/outcome_class.R                         15      11  26.67%   89-100
R/poisson_prior.R                         16       0  100.00%
R/prepare_stan_data_inputs.R              24       0  100.00%
R/prior_class.R                           26       8  69.23%   36-40, 60, 62, 77
R/sim_borrowing_list.R                    11       3  72.73%   78-80
R/sim_covariate_list.R                    17       4  76.47%   81-83, 99
R/sim_covariates.R                        29      20  31.03%   127-156
R/sim_data_list.R                         16       3  81.25%   203-205
R/sim_estimate_bias.R                      3       3  0.00%    79-81
R/sim_estimate_mse.R                       3       3  0.00%    79-81
R/sim_is_null_effect_covered.R             6       6  0.00%    78-83
R/sim_is_true_effect_covered.R             6       6  0.00%    82-87
R/sim_outcome_list.R                      11       3  72.73%   76-78
R/sim_samplesize.R                        18       6  66.67%   78-83
R/sim_treatment_list.R                    11       3  72.73%   74-76
R/simulation_class.R                      25      20  20.00%   54-73, 99
R/simvar_class.R                          24       4  83.33%   65-66, 165-166
R/treatment_class.R                        5       4  20.00%   33-36
R/treatment_details.R                      6       0  100.00%
R/trim_data_matrix.R                      11       0  100.00%
R/uniform_prior.R                         17       0  100.00%
R/weib_ph_surv_dist.R                     32       0  100.00%
R/zzz.R                                   19      18  5.26%    3-21
TOTAL                                   1078     252  76.62%

Diff against main

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

Results for commit: 795becbd12884a587a68a976da05174541493c77

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

github-actions[bot] commented 1 year ago

Unit Tests Summary

    1 files    38 suites   7m 9s :stopwatch: 193 tests 149 :heavy_check_mark: 44 :zzz: 0 :x: 607 runs  542 :heavy_check_mark: 65 :zzz: 0 :x:

Results for commit 4d7c90e6.

github-actions[bot] commented 1 year ago

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
cmdstan 💔 $10.49$ $+1.47$ $0$ $0$ $0$ $0$
create_analysis_obj 💔 $205.69$ $+28.44$ $0$ $0$ $0$ $0$
create_simulation_obj 💔 $162.55$ $+15.97$ $0$ $0$ $0$ $0$
Additional test case details | Test Suite | $Status$ | Time on `main` | $±Time$ | Test Case | |:-----|:----:|:----:|:----:|:-----| | cmdstan | 💔 | $10.49$ | $+1.47$ | check_cmdstanr_runs_as_expected | | create_analysis_obj | 💔 | $12.34$ | $+1.97$ | All_allowable_inputs_create_Analysis_object_borrowing_1_outcome_1_covariates_1_ | | create_analysis_obj | 💔 | $12.36$ | $+1.73$ | All_allowable_inputs_create_Analysis_object_borrowing_1_outcome_1_covariates_2_ | | create_analysis_obj | 💔 | $8.01$ | $+1.09$ | All_allowable_inputs_create_Analysis_object_borrowing_1_outcome_1_covariates_3_ | | create_analysis_obj | 💔 | $12.36$ | $+1.96$ | All_allowable_inputs_create_Analysis_object_borrowing_1_outcome_2_covariates_1_ | | create_analysis_obj | 💔 | $12.33$ | $+1.80$ | All_allowable_inputs_create_Analysis_object_borrowing_1_outcome_2_covariates_2_ | | create_analysis_obj | 💔 | $12.61$ | $+1.86$ | All_allowable_inputs_create_Analysis_object_borrowing_1_outcome_3_covariates_1_ | | create_analysis_obj | 💔 | $12.43$ | $+1.97$ | All_allowable_inputs_create_Analysis_object_borrowing_1_outcome_3_covariates_2_ | | create_analysis_obj | 💔 | $8.29$ | $+1.17$ | All_allowable_inputs_create_Analysis_object_borrowing_1_outcome_3_covariates_3_ | | create_analysis_obj | 💔 | $12.73$ | $+1.56$ | All_allowable_inputs_create_Analysis_object_borrowing_3_outcome_1_covariates_1_ | | create_analysis_obj | 💔 | $12.70$ | $+1.46$ | All_allowable_inputs_create_Analysis_object_borrowing_3_outcome_1_covariates_2_ | | create_analysis_obj | 💔 | $9.63$ | $+1.02$ | All_allowable_inputs_create_Analysis_object_borrowing_3_outcome_1_covariates_3_ | | create_analysis_obj | 💔 | $12.84$ | $+1.78$ | All_allowable_inputs_create_Analysis_object_borrowing_3_outcome_2_covariates_1_ | | create_analysis_obj | 💔 | $12.81$ | $+1.86$ | All_allowable_inputs_create_Analysis_object_borrowing_3_outcome_2_covariates_2_ | | create_analysis_obj | 💔 | $9.82$ | $+1.14$ | All_allowable_inputs_create_Analysis_object_borrowing_3_outcome_2_covariates_3_ | | create_analysis_obj | 💔 | $12.89$ | $+2.03$ | All_allowable_inputs_create_Analysis_object_borrowing_3_outcome_3_covariates_1_ | | create_analysis_obj | 💔 | $13.05$ | $+1.84$ | All_allowable_inputs_create_Analysis_object_borrowing_3_outcome_3_covariates_2_ | | create_analysis_obj | 💔 | $9.83$ | $+1.23$ | All_allowable_inputs_create_Analysis_object_borrowing_3_outcome_3_covariates_3_ | | create_simulation_obj | 💔 | $135.55$ | $+13.71$ | _create_simulation_obj_correct_inputs_create_Simulation_object | | create_simulation_obj | 💔 | $25.89$ | $+2.11$ | _create_simulation_obj_correctly_gets_number_of_combinations |

Results for commit 795becbd12884a587a68a976da05174541493c77

♻️ This comment has been updated with latest results.