baseline data simulation

[gravesti]

Pull Request

[github-actions]

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       1  93.75%   46
R/cmdstan.R                                7       2  71.43%   18-19
R/covariate_class.R                       11      10  9.09%    57-66
R/create_analysis_obj.R                   55       7  87.27%   61-64, 88-90
R/create_data_matrix.R                    24       0  100.00%
R/create_simulation_obj.R                 63      21  66.67%   94, 97, 100, 103, 122-131, 141-147
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%   62-86
R/half_cauchy_prior.R                     22       0  100.00%
R/half_normal_prior.R                     22       0  100.00%
R/helpers.R                               90       2  97.78%   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                           99      88  11.11%   72-304
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                           28       8  71.43%   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/simulate_data.R                        100      85  15.00%   22, 25, 69-358
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                         16       0  100.00%
R/weib_ph_surv_dist.R                     32       0  100.00%
R/zzz.R                                   19      18  5.26%    3-21
TOTAL                                   1226     366  70.15%

Diff against main

Filename             Stmts    Miss  Cover
-----------------  -------  ------  -------
R/cmdstan.R             +1      +2  -28.57%
R/simulate_data.R     +100     +85  +15.00%
TOTAL                 +101     +87  -5.05%

Results for commit: e1d7c23

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

    1 files    39 suites   2m 16s ⏱️
168 tests 128 ✔️ 40 💤 0 ❌
552 runs  489 ✔️ 63 💤 0 ❌

Results for commit 29245d6.

♻️ This comment has been updated with latest results.

[mattsecrest]

Thanks, @gravesti . I'll review today @mattsecrest

[mattsecrest]

@gravesti would you mind adding a functional vignette? I think the ones there are more like design documents and do not directly leverage the new functions. I can kind of figure it out from context but a proper vignette would help greatly.

[gravesti]

@mattsecrest See the new vignette data_simulation

[mattsecrest]

@gravesti thanks for the vignette, this looks great! Thanks so much for putting together. Just curious per my previous question on whether we want to overload add_covariates? Looks like it's still in there but not used in the simulation .Rmd?

[mattsecrest]

@gravesti after meeting: let's merge, review and clean redundant features after the fact.

[mattsecrest]

@gravesti after meeting: let's merge, review and clean redundant features after the fact.

And also see what the missing features are for survival