simaerep_inframe: simulate in dataframe

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

simulate in dataframe

Description

simulate in dataframe

Usage

simaerep_inframe(
  df_visit,
  r = 1000,
  under_only = FALSE,
  visit_med75 = FALSE,
  check = TRUE,
  param_site_aggr = list(method = "med75_adj", min_pat_pool = 0.2),
  param_eval_sites = list(method = "BH"),
  env = parent.frame()
)

Arguments

df_visit	Data frame with columns: study_id, site_number, patnum, visit, n_ae.
r	Integer or tbl_object, number of repetitions for bootstrap simulation. Pass a tbl object referring to a table with one column and as many rows as desired repetitions. Default: 1000.
under_only	Logical, compute under-reporting probabilities only. Supersedes under_only parameter passed to eval_sites() and sim_sites(). Default: TRUE.
visit_med75	Logical, should evaluation point visit_med75 be used. Default: TRUE.
check	Logical, perform data check and attempt repair with check_df_visit(). Computationally expensive on large data sets. Default: TRUE.
param_site_aggr	List of parameters passed to site_aggr(). Default: list(method = "med75_adj", min_pat_pool = 0.2).
param_eval_sites	List of parameters passed to eval_sites(). Default: list(method = "BH").
env	Optional, provide environment of original visit data. Default: parent.frame().

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"

simaerep_inframe(df_visit)
simaerep_inframe(df_visit, visit_med75 = TRUE)$df_eval

# Database
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = ":memory:")
df_r <- tibble::tibble(rep = seq(1, 1000))

dplyr::copy_to(con, df_visit, "visit")
dplyr::copy_to(con, df_r, "r")

tbl_visit <- dplyr::tbl(con, "visit")
tbl_r <- dplyr::tbl(con, "r")

simaerep_inframe(tbl_visit, r = tbl_r)$df_eval
simaerep_inframe(tbl_visit, r = tbl_r, visit_med75 = TRUE)$df_eval

DBI::dbDisconnect(con)

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