R/varfreq_obs_freq.R

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

##' Calculate observed variant prevalence
##'
##' This function calculates the observed variant prevalence from the coefficient of detection ratio
##' and the actual variant prevalence. 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 of observed prevalence of variant 1
##'
##' @author Shirlee Wohl, Elizabeth C. Lee, Bethany L. DiPrete, and Justin Lessler
##'
##' @examples
##' varfreq_obs_freq(p_v1 = 0.1, c_ratio = 1.1)
##'
##' @family variant frequency functions
##'
##' @export


varfreq_obs_freq <- 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")

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