R/Adjusted_inv_sinh_CI_OR_2x2.R

In ocbe-uio/contingencytables: Statistical Analysis of Contingency Tables

#' @title The adjusted inverse hyperbolic sine confidence interval for the odds
#' ratio
#' @description The adjusted inverse hyperbolic sine confidence interval for
#' the odds ratio.
#' @description Described in Chapter 4 "The 2x2 Table"
#' @param n the observed counts (a 2x2 matrix)
#' @param psi1 pseudo-frequency (should be > 0)
#' @param psi2 pseudo-frequency (should be > 0)
#' @param alpha the nominal level, e.g. 0.05 for 95% CIs
#' @return An object of the [contingencytables_result] class,
#' basically a subclass of [base::list()]. Use the [utils::str()] function
#' to see the specific elements returned.
#' @examples
#' Adjusted_inv_sinh_CI_OR_2x2(lampasona_2013)
#' Adjusted_inv_sinh_CI_OR_2x2(ritland_2007)
#' @export
Adjusted_inv_sinh_CI_OR_2x2 <- function(
  n, psi1 = 0.45, psi2 = 0.25, alpha = 0.05
) {
  validateArguments(mget(ls()))

  # Estimate of the odds ratio (thetahat)
  estimate <- n[1, 1] * n[2, 2] / (n[1, 2] * n[2, 1])

  # Adjusted estimate
  thetatilde <- (n[1, 1] + psi1) * (n[2, 2] + psi1) / ((n[1, 2] + psi1) * (n[2, 1] + psi1))

  # The upper alpha / 2 percentile of the standard normal distribution
  z <- qnorm(1 - alpha / 2, 0, 1)

  # Calculate the confidence limits
  tmp <- asinh(
    0.5 * z *
    sqrt(
      1 / (n[1, 1] + psi2) + 1 / (n[1, 2] + psi2) + 1 / (n[2, 1] + psi2) + 1 / (n[2, 2] + psi2)
    )
  )
  L <- exp(log(thetatilde) - 2 * tmp)
  U <- exp(log(thetatilde) + 2 * tmp)

  # Output
  printresults <- function() {
    cat_sprintf(
      "The adjusted inverse sinh CI: estimate = %6.4f (%g%% CI %6.4f to %6.4f)",
      estimate, 100 * (1 - alpha), L, U
    )
  }

  return(
    contingencytables_result(
      list("lower" = L, "upper" = U, "estimate" = estimate), printresults
    )
  )
}