R/translink_prob_transmit.R

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

##' Calculate probability of transmission
##'
##' This function calculates the probability that two cases are linked by direct transmission
##' given that they have been linked by phylogenetic criteria.
##' Assumptions about transmission and linkage (single or multiple) can be specified.
##'
##' @param sensitivity scalar or vector giving the sensitivity of the linkage criteria
##' @param specificity scalar or vector giving the specificity of the linkage criteria
##' @param rho scalar or vector giving the proportion of the final outbreak size that is sampled
##' @param M scalar or vector giving the number of cases sampled
##' @param R scalar or vector giving the effective reproductive number of the pathogen
##' @param assumption a character vector indicating which assumptions about transmission and linkage criteria. Default = `'mtml'`. Accepted arguments are:
##' \enumerate{
##'      \item `'stsl'` for the single-transmission single-linkage assumption.
##'      \item `'mtsl'` for the multiple-transmission single-linkage assumption.
##'      \item `'mtml'` for the multiple-transmission multiple-linkage assumption.
##'      }
##'
##' @return scalar or vector giving the probability of transmission between two cases given linkage by phylogenetic criteria
##'
##' @author John Giles, Shirlee Wohl, and Justin Lessler
##'
##' @examples
##' translink_prob_transmit(sensitivity=0.99, specificity=0.9, rho=0.5, M=100, R=1)
##'
##' @family transmission linkage functions
##'
##' @export
##'

translink_prob_transmit <- function(sensitivity, specificity, rho, M, R, assumption = "mtml") {
    if (assumption == "stsl") {
        message("Calculating probability of transmission assuming single-transmission and single-linkage")
        out <- translink_prob_transmit_stsl(sensitivity = sensitivity, specificity = specificity,
            rho = rho, M = M)
    } else if (assumption == "mtsl") {
        message("Calculating probability of transmission assuming multiple-transmission and single-linkage")
        out <- translink_prob_transmit_mtsl(sensitivity = sensitivity, specificity = specificity,
            rho = rho, M = M, R = R)
    } else if (assumption == "mtml") {
        message("Calculating probability of transmission assuming multiple-transmission and multiple-linkage")
        out <- translink_prob_transmit_mtml(sensitivity = sensitivity, specificity = specificity,
            rho = rho, M = M, R = R)
    } else {
        stop("Incorrect assumption argument")
    }

    return(out)
}