Tweaks for cran

[mattsecrest]

No response form Uwe yet let's see if this fixes things. cran-submit-2.pdf

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```diff @@ Coverage Diff @@ ## main #278 +/- ## ========================================== + Coverage 79.41% 79.54% +0.12% ========================================== Files 60 60 Lines 1613 1613 ========================================== + Hits 1281 1283 +2 + Misses 332 330 -2 ```

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[mattsecrest]

Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g. \value{No return value, called for side effects} or similar) Missing Rd-tags:

• [x] bernoulli_prior.Rd: \value
• [x] beta_prior.Rd: \value
• [x] bin_var.Rd: \value
• [x] borrowing_details.Rd: \value
• [x] cauchy_prior.Rd: \value
• [x] cont_var.Rd: \value
• [x] create_alpha_string.Rd: \value
• [x] create_tau_string.Rd: \value
• [x] eval_constraints.Rd: \value
• [x] exp_surv_dist.Rd: \value
• [x] exponential_prior.Rd: \value
• [x] gamma_prior.Rd: \value
• [x] generate.Rd: \value
• [x] get_cmd_stan_models.Rd: \value
• [x] get_results.Rd: \value
• [x] half_cauchy_prior.Rd: \value
• [x] half_normal_prior.Rd: \value
• [x] logistic_bin_outcome.Rd: \value
• [x] normal_prior.Rd: \value
• [x] plot_pdf.Rd: \value
• [x] plot_pmf.Rd: \value
• [x] plot.Rd: \value
• [x] poisson_prior.Rd: \value
• [x] show_guide.Rd: \value
• [x] sim_borrowing_list.Rd: \value
• [x] sim_covariate_list.Rd: \value
• [x] sim_data_list.Rd: \value
• [x] sim_outcome_list.Rd: \value
• [x] sim_treatment_list.Rd: \value
• [x] trim_cols.Rd: \value
• [x] trim_rows.Rd: \value
• [x] weib_ph_surv_dist.Rd: \value

[mattsecrest]

You have examples for unexported functions. Please either omit these examples or export these functions. Examples for unexported function

• [x] c() in:

  add_covariates.Rd baseline_covariates.Rd check_data_matrix_has_columns.Rd covariance_matrix.Rd create_analysis_obj.Rd create_baseline_object.Rd create_data_matrix.Rd create_data_simulation.Rd create_simulation_obj.Rd enrollment_constant.Rd generate-BaselineObject-method.Rd generate-DataSimObject-method.Rd get_covariate_constraints.Rd mcmc_sample.Rd plot.Rd rename_draws_covariates.Rd set_enrollment.Rd sim_covariate_list.Rd sim_data_list.Rd

[mattsecrest]

"Using foo:::f instead of foo::f allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance."

• [x] Used ::: in documentation:

  man/check_data_matrix_has_columns.Rd man/get_covariate_constraints.Rd man/get_prior_string.Rd man/make_model_string_data.Rd etc.... Please omit one colon.

[mattsecrest]

\dontrun{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \dontrun{} adds the comment ("# Not run:") as a warning for the user. Does not seem necessary. Please replace \dontrun with \donttest. Please unwrap the examples if they are executable in < 5 sec, or replace dontrun{} with \donttest{}.

• [ ] -> mcmc_sample.Rd

[mattsecrest]

We still see: Examples for unexported function

• [x] generate() in get_prior_string.Rd
• [x] get_stan_code() in: make_model_string_data.Rd
• [x] get_vars() in: make_model_string_functions.Rd
• [x] half_normal_prior() in: make_model_string_parameters.Rd
• [x] logistic_bin_outcome() in: make_model_string_transf_param.Rd
• [x] outcome_bin_logistic() in: parse_constraint.Rd

Please either omit these examples or export these functions.

[mattsecrest]

Some code lines in examples are commented out. Please never do that. Ideally find toy examples that can be regularly executed and checked. Lengthy examples (> 5 sec), can be wrapped in \donttest{}. Examples in comments in:

• [x] get_prior_string.Rd
• [x] make_model_string_data.Rd
• [x] make_model_string_functions.Rd
• [x] make_model_string_parameters.Rd
• [x] make_model_string_transf_param.Rd
• [x] parse_constraint.Rd
• [ ] prior_gamma.Rd
• [ ] prior_normal.Rd
• [ ] treatment_details.Rd

[mattsecrest]

Per Daniel Sjoberg's suggestions just wrapping in @noRd and pushing back on prior_gamma, prior_normal, and treatment_details, which do not have commented out examples.

[mattsecrest]

@danielinteractive @gravesti the package as-is was accepted to CRAN. Would someone be able to approve so I can move aditional tweaks to a new branch?