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

simaerep

R Documentation

Create simaerep object

Description

Simulate AE under-reporting probabilities.

Usage

simaerep(
  df_visit,
  r = 1000,
  check = TRUE,
  under_only = TRUE,
  visit_med75 = TRUE,
  inframe = FALSE,
  progress = TRUE,
  mult_corr = TRUE,
  param_site_aggr = list(method = "med75_adj", min_pat_pool = 0.2),
  param_sim_sites = list(r = 1000, poisson_test = FALSE, prob_lower = TRUE),
  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.
`check`	Logical, perform data check and attempt repair with `check_df_visit()`. Computationally expensive on large data sets. Default: TRUE.
`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.
`inframe`	Logical, only table operations to be used; does not require visit_med75. Compatible with dbplyr supported database backends.
`progress`	Logical, display progress bar. Default: TRUE.
`mult_corr`	Logical, multiplicity correction, Default: TRUE
`param_site_aggr`	List of parameters passed to `site_aggr()`. Default: list(method = "med75_adj", min_pat_pool = 0.2).
`param_sim_sites`	List of parameters passed to `sim_sites()`. Default: list(r = 1000, poisson_test = FALSE, prob_lower = TRUE).
`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().

Details

Executes site_aggr(), sim_sites(), and eval_sites() on original visit data and stores all intermediate results. Stores lazy reference to original visit data for facilitated plotting using generic plot(x).

Value

A simaerep object.

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"
aerep <- simaerep(df_visit)
aerep
str(aerep)

  # In-frame table operations
  simaerep(df_visit, inframe = TRUE, visit_med75 = FALSE, under_only = FALSE)$df_eval
  simaerep(df_visit, inframe = TRUE, visit_med75 = TRUE, under_only = FALSE)$df_eval
  # Database example
  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(tbl_visit, r = tbl_r, inframe = TRUE, visit_med75 = FALSE, under_only = FALSE)$df_eval
  simaerep(tbl_visit, r = tbl_r, inframe = TRUE, visit_med75 = TRUE, under_only = FALSE)$df_eval
  DBI::dbDisconnect(con)

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