R/get_ACC.R

In toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

#' Get the ACC values for a selection of chemicals
#'
#' The \code{get_ACC} function retrieves the activity concentration at cutoff
#' (ACC) values for specified chemicals.
#'
#' The data used in toxEval were combined from files in the
#' "INVITRODB_V3_LEVEL5" directory that were included in the October 2018
#' release of the ToxCast database. The function \code{get_ACC} will
#' convert the ACC values in the ToxCast database from units of (log \eqn{\mu}M)
#' to units of \eqn{\mu}g/L, and reformat the data as input to toxEval.
#'
#' @param CAS Vector of CAS.
#' @import dplyr
#'
#' @return data frame with columns CAS, chnm, flags, endPoint, ACC, MlWt, and ACC_value
#' @export
#' @examples
#' CAS <- c("121-00-6", "136-85-6", "80-05-7", "84-65-1", "5436-43-1", "126-73-8")
#' ACC <- get_ACC(CAS)
#' head(ACC)
get_ACC <- function(CAS) {

  # Getting rid of NSE warnings:
  Structure_MolWt <- Substance_CASRN <- casn <- Substance_Name <- ".dplyr"
  chnm <- flags <- MlWt <- ACC_value <- casrn <- endPoint <- ".dplyr"

  chem_list <- dplyr::select(tox_chemicals,
    casrn = Substance_CASRN,
    MlWt = Structure_MolWt
  )
  chem_list <- dplyr::filter(chem_list, casrn %in% CAS)

  ACC <- ToxCast_ACC
  ACC <- dplyr::filter(ACC, CAS %in% CAS)
  ACC <- dplyr::right_join(ACC, chem_list,
    by = c("CAS" = "casrn")
  )

  ACC <- mutate(ACC,
    ACC_value = 10^ACC,
    ACC_value = ACC_value * MlWt
  )
  ACC <- filter(ACC, !is.na(ACC_value))
  ACC <- left_join(ACC, select(tox_chemicals,
    CAS = Substance_CASRN,
    chnm = Substance_Name
  ), by = "CAS")

  if (any(is.na(ACC$MlWt))) {
    warning("Some chemicals are missing molecular weights")
  }

  return(ACC)
}