R/varfreq_expected_mbias.R

In HopkinsIDD/phylosamp: Sample Size Calculations for Molecular and Phylogenetic Studies

##' Calculate multiplicative bias (observed / actual) in variant prevalence
##'
##' This function calculates the multiplicative bias of the observed variant proportion
##' relative to the actual variant proportion. This function assumes that variant 1 is the variant of concern.
##' This function is specific to the two-variant system.
##'
##' @param p_v1 actual variant prevalence (proportion)
##' @param c_ratio coefficient of detection ratio, calculated as the ratio of the coefficients of variant 1 to variant 2
##' @return scalar giving the multiplicative bias of variant 1
##'
##' @author Shirlee Wohl, Elizabeth C. Lee, Bethany L. DiPrete, and Justin Lessler
##'
##' @examples
##' varfreq_expected_mbias(p_v1 = 0.1, c_ratio = 1.1)
##'
##' @family variant frequency functions
##'
##' @export


varfreq_expected_mbias <- function(p_v1, c_ratio) {
  if (!all(is.numeric(p_v1), p_v1 > 0 & p_v1 < 1)) stop("Variant prevalence must be numeric and between 0 and 1.")
  if (!all(is.numeric(c_ratio), c_ratio > 0)) stop("Coefficient of detection ratio must be numeric and greater than 0")

  bias <- p_v1 + ((1 / c_ratio) * (1 - p_v1))
  return(1 / bias)
}