R/cv_to_omega.R

In InsightRX/PKPDsim: Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations

#' Create lower-diagonal omega matrix from CV for parameter estimates
#'
#' @param par_cv list of parameter CVs
#' @param parameters list of parameters
#' @return a vector describing the lower triangle of the omega (between-subject variability) matrix
#' @export
#' @seealso \link{sim_ode}

cv_to_omega <- function(par_cv = NULL, parameters = NULL) {
  if (is.null(par_cv) || !("list" %in% class(par_cv))) {
    stop("List of coefficients of variation required as argument to cv_to_omega().")
  }
  if(is.null(names(par_cv))) {
    stop("`par_cv` should be a named list.")
  }
  if(is.null(parameters)) {
    nam <- names(par_cv)
    message(paste0("No parameter list provided as argument, assumed order for `omega_matrix`: ", paste(nam, collapse=", ")))
  } else {
    nam <- names(parameters)
  }
  omega <- c()
  for (i in 1:length(nam)) {
    if (nam[i] %in% names(par_cv)) {
      om_diag <- (par_cv[[nam[i]]])^2
    } else {
      om_diag <- 0
    }
    omega <- c(omega, c(rep(0, i-1), om_diag))
  }
  return(omega)
}