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#' Load CLint and Fup QSPR predictions predictions from Pradeep et al. 2020.
#'
#' This function returns an updated version of
#' \code{\link{chem.physical_and_invitro.data}}
#' that includes quantitative
#' structure-property relationship (QSPR) predictions from
#' Support Vector Machine and Random Forest
#' models developed and presented in Pradeep et al. 2020, included in
#' \code{\link{pradeep2020}}.
#'
#' Because Clint and Fup are the only measurements required for many HTTK models,
#' changing the number of chemicals for which a value is available will change
#' the number of chemicals which are listed with the \code{\link{get_cheminfo}}
#' command. Use the command \code{\link{reset_httk}} to return to the initial
#' (measured only) \code{\link{chem.physical_and_invitro.data}} (for all
#' parameters).
#'
#' @param overwrite Only matters if load.image=FALSE. If overwrite=TRUE then
#' existing data in chem.physical_and_invitro.data will be replaced by any
#' predictions in Pradeep et al. (2020) that is for the same chemical and
#' property. If overwrite=FALSE (DEFAULT) then new data for the same chemical
#' and property are ignored. Funbound.plasma values of 0 (below limit of
#' detection) are overwritten either way.
#'
#' @param target.env The environment where the new
#' \code{\link{chem.physical_and_invitro.data}} is loaded. Defaults to global environment.
#'
#' @return \item{data.frame}{An updated version of
#' \code{\link{chem.physical_and_invitro.data}}.}
#'
#' @seealso \code{\link{reset_httk}}
#' @seealso \code{\link{get_cheminfo}}
#'
#' @author Sarah E. Davidson
#'
#' @references
#' \insertRef{pradeep2020chemstr}{httk}
#'
#' @examples
#'
#' \dontrun{
#' # Count how many chemicals for which HTTK is available without the QSPR:
#' num.chems <- length(get_cheminfo())
#' print(num.chems)
#'
#' # For chemicals with Pradeep et al. (2020) Clint and Fup QSPR predictions,
#' # add them to our chemical information wherever measured values are
#' # unavailable:
#' load_pradeep2020()
#'
#' # Or, for chemicals with Pradeep et al. (2020) QSPR predictions, add them to
#' # our chemical information but overwrite measured values where we had them:
#' load_pradeep2020(overwrite=TRUE)
#'
#' # Let's see how many chemicals we have now with the Pradeep et al. (2020)
#' # predictions data loaded:
#' length(get_cheminfo())
#'
#' # Now let us reset the chemical data to the initial version:
#' reset_httk()
#'
#' # We should be back to our original number:
#' num.chems == length(get_cheminfo())
#' }
#'
#' @export load_pradeep2020
load_pradeep2020 <- function(
overwrite=FALSE,
target.env=.GlobalEnv)
{
cat(paste("Loading CLint and Fup predictions from Pradeep et al. (2020) for",
dim(httk::pradeep2020)[1],"chemicals.\n"))
cat(paste("Existing data are",
ifelse(overwrite,""," not"),
" being overwritten.\n",sep=""))
cat("Please wait...\n")
assign("chem.physical_and_invitro.data",
add_chemtable(httk::pradeep2020,
current.table=chem.physical_and_invitro.data,
data.list=list(
CAS = 'CASRN',
DTXSID='DTXSID',
Funbound.plasma = 'Consensus (SVM,RF)',
Clint = 'pred_clint_rf'),
reference = 'Pradeep 2020',
species= 'Human',
overwrite=overwrite),
envir=target.env)
}
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