Correct under-reporting probabilities using p.adjust
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eval_sites(df_sim_sites, method = "BH", ...)
df_sim_sites | dataframe generated by |
---|---|
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() |
dataframe with the following columns:
study identification
site identification
median(max(visit)) * 0.75
mean AE at visit_med75 site level
mean AE at visit_med75 study level
p-value as returned by poisson.test
bootstrapped probability for having mean_ae_site_med75 or lower
adjusted p-values
adjusted bootstrapped probability for having mean_ae_site_med75 or lower
probability under-reporting as 1 - pval_adj, poisson.test (use as benchmark)
probability under-reporting as 1 - prob_low_adj, bootstrapped (use)
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 adjustmentdf_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>