eval_sites: Evaluate sites.

In openpharma/simaerep: Find Clinical Trial Sites Under-Reporting Adverse Events

Evaluate sites.

Description

Correct under-reporting probabilities using p.adjust.

Usage

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

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"
under_only	compute under-reporting probabilities only, default = TRUE check_df_visit(), computationally expensive on large data sets. Default: TRUE
...	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

site_aggr, sim_sites, p.adjust

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

openpharma/simaerep documentation built on Feb. 2, 2025, 12:04 a.m.