Skip to contents

Calculate prob_lower and poisson.test pvalue for study sites.

Source: R/simaerep.R
sim_sites.Rd

Collects the number of AEs of all eligible patients that meet visit_med75 criteria of site. Then calculates poisson.test pvalue and bootstrapped probability of having a lower mean value.

Usage

sim_sites(
  df_site,
  df_visit,
  r = 1000,
  poisson_test = TRUE,
  prob_lower = TRUE,
  progress = TRUE,
  check = TRUE,
  under_only = TRUE
)

Arguments

df_site

dataframe created by site_aggr

df_visit

dataframe, created by sim_sites

r

integer, denotes number of simulations, default = 1000

poisson_test

logical, calculates poisson.test pvalue

prob_lower

logical, calculates probability for getting a lower value

progress

logical, display progress bar, Default = TRUE

check,

logical, perform data check and attempt repair with

under_only

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

Value

dataframe with the following columns:

study_id

study identification

site_number

site identification

n_pat

number of patients at site

visit_med75

median(max(visit)) * 0.75

n_pat_with_med75

number of patients at site with med75

mean_ae_site_med75

mean AE at visit_med75 site level

mean_ae_study_med75

mean AE at visit_med75 study level

n_pat_with_med75_study

number of patients at study with med75 excl. site

pval

p-value as returned by poisson.test

prob_low

bootstrapped probability for having mean_ae_site_med75 or lower

See also

sim_sites, site_aggr, pat_pool, prob_lower_site_ae_vs_study_ae, poiss_test_site_ae_vs_study_ae, sim_sites, prep_for_sim

Examples

df_visit <- sim_test_data_study(
   n_pat = 100,
   n_sites = 5,
   frac_site_with_ur = 0.4,
   ur_rate = 0.2
)

df_visit$study_id <- "A"

df_site <- site_aggr(df_visit)

df_sim_sites <- sim_sites(df_site, df_visit, r = 100)

df_sim_sites %>%
 knitr::kable(digits = 2)
#> 
#> 
#> |study_id |site_number | n_pat| n_pat_with_med75| visit_med75| mean_ae_site_med75| mean_ae_study_med75| n_pat_with_med75_study| pval| prob_low|
#> |:--------|:-----------|-----:|----------------:|-----------:|------------------:|-------------------:|----------------------:|----:|--------:|
#> |A        |S0001       |    20|               20|          15|               6.35|                6.31|                     71| 1.00|     1.00|
#> |A        |S0002       |    20|               19|          15|               5.37|                6.57|                     72| 0.06|     0.06|
#> |A        |S0003       |    20|               18|          15|               7.11|                6.12|                     73| 1.00|     1.00|
#> |A        |S0004       |    20|               15|          17|               7.87|                7.03|                     61| 1.00|     1.00|
#> |A        |S0005       |    20|               19|          15|               6.37|                6.31|                     72| 1.00|     1.00|