pvEBayes (version 0.2.1)

generate_contin_table: Generate random contingency tables based on a reference table embedded signals,and possibly with zero inflation

Description

This function generates random contingency tables that resemble a given reference table, with the option to embed signals and zero-inflation.

Usage

generate_contin_table(
  n_table = 1,
  ref_table,
  signal_mat = NULL,
  Variation = FALSE,
  zi_indic_mat = NULL
)

Value

A list of length n_table, with each entry being a nrow(ref_table) by ncol(ref_table) matrix.

Arguments

n_table

a number of random matrices to generate.

ref_table

a reference table used as the basis for generating random tables.

signal_mat

a numeric matrix of the same dimension as the reference table (ref_table). The entry at position (i, j) in signal_mat represents the signal strength between the i-th adverse event and the j-th drug. By default, each pair is assigned a value of 1, indicating no signal for that pair.

Variation

logical. Include random noises to sig_mat while generating random tables. Default to FALSE. If set to TRUE, n_table of sig_mat incorporating the added noise will also be returned.

zi_indic_mat

logical matrix of the same size as ref_table indicating the positions of structural zero.

References

Tan Y, Markatou M and Chakraborty S. Flexible Empirical Bayesian Approaches to Pharmacovigilance for Simultaneous Signal Detection and Signal Strength Estimation in Spontaneous Reporting Systems Data. Statistics in Medicine. 2025; 44: 18-19, https://doi.org/10.1002/sim.70195.

Examples

set.seed(1)
ref_table <- statin2025_44


# set up signal matrix with one signal at entry (1,1)
sig_mat <- matrix(1, nrow(ref_table), ncol(ref_table))
sig_mat[1, 1] <- 2

# set up structural zero matrix
Z <- matrix(0, nrow(ref_table), ncol(ref_table))
Z[5, 1] <- 1

simu_table <- generate_contin_table(ref_table,
  signal_mat = sig_mat,
  n_table = 1,
  Variation = TRUE,
  zi_indic_mat = Z
)[[1]][[1]]