R/post_hit_AUC.R

In USEPA/CompTox-ToxCast-tcplFit2: A Concentration-Response Modeling Utility

#' Calculate Area Under the Curve After Hit-calling
#'
#' Function that calculates the area under the curve (AUC) after hit-calling.
#'
#' This function calculates the area under the curve (AUC) for the winning model
#' selected during hit-calling. Wrapper function for `get_AUC`.
#' Designed to take the one-row output from `tcplhit2_core`, parse the model
#' details, and pass these values to `get_AUC` to estimate the AUC for the
#' winning model.
#'
#' @param hit_results output from `tcplhit2_core`.
#' @param return.abs Logical argument, if TRUE, returns the absolute value of the AUC. Defaults to FALSE.
#' @param use.log Logical argument, defaults to FALSE. By default, the function estimates AUC with
#' concentrations in normal unit. If set to TRUE, will use concentration in log10-scale for
#' estimating AUC.
#'
#' @return AUC value of the winning model (numeric)
#'
#' @seealso get_AUC
#'
#' @export
#' @importFrom stringr str_split
#'
#' @examples
#'
#' conc <- c(.03, .1, .3, 1, 3, 10, 30, 100)
#' resp <- c(0, .2, .1, .4, .7, .9, .6, 1.2)
#' params <- tcplfit2_core(conc, resp, .8)
#' output <- tcplhit2_core(params, conc, resp, 0.8, 0.5)
#' post_hit_AUC(output)
#'
#'
post_hit_AUC <- function(hit_results, return.abs = FALSE, use.log = FALSE) {

  # parameter list
  param <- c("a","tp","b","ga","p", "la", "q", "er")

  # get concentrations
  conc <- as.numeric(str_split(hit_results[1,"conc"],"\\|")[[1]])
  # get fitted values of the winning model
  modpars <- unlist(hit_results[1, param])
  modpars <- modpars[!is.na(modpars)]
  # get the winning model name
  fit_method <- hit_results[["fit_method"]]
  out <- get_AUC(fit_method, min(conc), max(conc), ps = modpars,
                 return.abs = return.abs,
                 use.log = use.log)

  # return AUC
  return(out)

}