R/lpDataSim.R

In ku-awdc/eggSim: Simulating Datasets Representing Egg Reduction Rate Data

#' Simulate ERR data from a correlated lognormal distribution
#'
#' @param N The number of (paired) observations to simulate
#' @param mu_pre The pre-treatment arithmetic mean eggs per gram
#' @param mu_post The post-treatment arithmetic mean eggs per gram
#' @param cv_pre The extra-Poisson coefficient of variation (ratio of standard deviation to mean) in the pre-treatment data
#' @param cv_post The extra-Poisson coefficient of variation (ratio of standard deviation to mean) in the post-treatment data
#' @param correlation The extra-Poisson correlation between pre- and post-treatment log-lambda parameters
#' @param parameters Alternative way to specify the parameters as output of the ERRparameters function
#'
#' @return A data frame containing the simulated data
#'
#' @examples
#' lpDataSim(10, 10, 1, 1, 1, 0.4)
#'
#' @importFrom MASS mvrnorm
#'
#' @export
lpDataSim <- function(N, mu_pre, mu_post, cv_pre, cv_post, correlation, parameters=NULL){

  stopifnot(length(N) == 1 && N > 0)
  stopifnot(length(mu_pre) == 1 && mu_pre > 0)
  stopifnot(length(mu_post) == 1 && mu_post >= 0)
  stopifnot(length(cv_pre) == 1 && cv_pre > 0)
  stopifnot(length(cv_post) == 1 && cv_post > 0)
  stopifnot(length(correlation) == 1 && correlation >= 0 && correlation <= 1)

  if(!is.null(parameters)){
    stopifnot(!is.null(parameters$lnormals))
  }else{
    parameters <- ERRparameters(mu_pre, mu_post, cv_pre, cv_post, correlation, FALSE)
  }

  lrates <- mvrnorm(N, parameters$lnormals$lmus, parameters$lnormals$sigma)
  pre <- exp(lrates[,1])
  post <- exp(lrates[,2])

  return(data.frame(ID = 1:N, preLambda = pre, postLambda = post))

}