Correct under-reporting probabilities using p.adjust.

eval_sites(df_sim_sites, method = "BH", ...)

Arguments

df_sim_sites

dataframe generated by sim_sites

method

character, passed to stats::p.adjust(), if NULL eval_sites_deprecated() is used instead, Default = "BH"

...

use to pass r_sim_sites parameter to eval_sites_deprecated()

Value

dataframe with the following columns:

study_id

study identification

site_number

site identification

visit_med75

median(max(visit)) * 0.75

mean_ae_site_med75

mean AE at visit_med75 site level

mean_ae_study_med75

mean AE at visit_med75 study level

pval

p-value as returned by poisson.test

prob_low

bootstrapped probability for having mean_ae_site_med75 or lower

pval_adj

adjusted p-values

prob_low_adj

adjusted bootstrapped probability for having mean_ae_site_med75 or lower

pval_prob_ur

probability under-reporting as 1 - pval_adj, poisson.test (use as benchmark)

prob_low_prob_ur

probability under-reporting as 1 - prob_low_adj, bootstrapped (use)

See also

Examples

df_visit <- sim_test_data_study(n_pat = 100, n_sites = 5, frac_site_with_ur = 0.4, ur_rate = 0.6) df_visit$study_id <- "A" df_site <- site_aggr(df_visit) df_sim_sites <- sim_sites(df_site, df_visit, r = 100) df_eval <- eval_sites(df_sim_sites) df_eval
#> # A tibble: 5 × 14 #> study_id site_number n_pat n_pat_with_med75 visit_med75 mean_ae_site_med75 #> <chr> <chr> <int> <int> <dbl> <dbl> #> 1 A S0002 20 16 16 2.75 #> 2 A S0001 20 16 15 2.62 #> 3 A S0003 20 19 15 6.37 #> 4 A S0004 20 16 16 7.81 #> 5 A S0005 20 17 16 8.59 #> # … with 8 more variables: mean_ae_study_med75 <dbl>, #> # n_pat_with_med75_study <int>, pval <dbl>, prob_low <dbl>, pval_adj <dbl>, #> # pval_prob_ur <dbl>, prob_low_adj <dbl>, prob_low_prob_ur <dbl>
# use deprecated method ------- df_eval <- eval_sites(df_sim_sites, method = NULL, r_sim_sites = 100)
#> Warning: using deprecated method for probability adjustment
df_eval
#> # A tibble: 5 × 19 #> study_id site_number n_pat n_pat_with_med75 visit_med75 mean_ae_site_med75 #> <chr> <chr> <int> <int> <dbl> <dbl> #> 1 A S0002 20 16 16 2.75 #> 2 A S0001 20 16 15 2.62 #> 3 A S0003 20 19 15 6.37 #> 4 A S0004 20 16 16 7.81 #> 5 A S0005 20 17 16 8.59 #> # … with 13 more variables: mean_ae_study_med75 <dbl>, #> # n_pat_with_med75_study <int>, pval <dbl>, prob_low <dbl>, n_site <int>, #> # pval_n_detected <int>, pval_fp <dbl>, pval_p_vs_fp_ratio <dbl>, #> # pval_prob_ur <dbl>, prob_low_n_detected <int>, prob_low_fp <dbl>, #> # prob_low_p_vs_fp_ratio <dbl>, prob_low_prob_ur <dbl>