R/cutpoint.R

In cfree14/nutriR: Nutritional intake functions for R

#' Calculate prevalence of inadequate intakes using the cutpoint method
#'
#' This function calculates the prevalence of inadequate intakes using the EAR cutpoint method.
#'
#' @param intake_avg Mean of the habitual intake distribution
#' @param intake_cv Coefficient of variation (CV) of the habitual intake distribution
#' @param intake_dist Type of the habitual intake distribution: normal, lognormal, or gamma
#' @param ear Estimated Average Requirement (EAR)
#' @return The percent of a population with inadequate nutrient intakes (SEV)
#' @examples
#' cutpoint(intake_avg=6, intake_cv=0.25, intake_dist="normal", ear=8)
#' cutpoint(intake_avg=6, intake_cv=0.25, intake_dist="gamma", ear=8)
#' cutpoint(intake_avg=6, intake_cv=0.25, intake_dist="lognormal", ear=8)
#' @export
cutpoint <- function(intake_avg, intake_cv, intake_dist, ear){

  # Check distribution
  dist_check <- intake_dist %in% c("normal", "lognormal", "gamma")
  if(!dist_check){
    warning("Intake distribution must be one of the following: normal, lognormal, or gamma")
    pdeficient <- NA
  }else{

    # Normal distribution
    if(intake_dist=="normal"){
      pdeficient <- pnorm(q=ear, mean=intake_avg, sd=intake_avg*intake_cv) * 100
    }

    # Gamma distribution
    if(intake_dist=="lognormal"){
      sdlog <- sqrt(log(intake_cv^2+1))
      meanlog <- log(intake_avg) - sdlog^2/2
      pdeficient <- plnorm(q=ear, meanlog=meanlog, sdlog=sdlog) * 100
    }

    # Gamma distribution
    if(intake_dist=="gamma"){
      shape <- (1 / intake_cv) ^ 2
      rate <- shape / intake_avg
      pdeficient <- pgamma(q=ear, shape=shape, rate=rate) * 100
    }

  }

  # Return
  return(pdeficient)

}