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#' Return the assumptions used in Honda et al. 2019
#'
#' This function returns four of the better performing sets of assumptions evaluated in Honda et al. 2019
#' (https://doi.org/10.1371/journal.pone.0217564).These include four different combinations of hepatic clearance assumption, in vivo bioactivity assumption,
#' and relevant tissue assumption. Generally, this function is not called directly by the user, but instead
#' called by setting the IVIVE option in calc_mc_oral_equiv, calc_mc_css, and calc_analytic functions. Currently, these IVIVE option
#' is not implemented the solve_1comp etc. functions.
#'
#' @param method This is set to one of "Honda1", "Honda2", "Honda3", or "Honda4".
#' @param tissue This is only relevant to "Honda4" and indicates the relevant tissue compartment.
#' @return A list of tissue, bioactive.free.invivo, and restrictive.clearance assumptions.
#'
#' @details
#'
#' Only four sets of IVIVE assumptions that performed well in Honda et al.
#' (2019) are currently included:
#' "Honda1" through "Honda4". The use of max (peak)
#' concentration can not be currently be calculated with \code{\link{calc_analytic_css}}.
#' The httk default settings correspond to "Honda3":
#'
#'\tabular{lrrrrr}{
#' \tab \emph{In Vivo} Conc. \tab Metabolic Clearance \tab Bioactive Chemical Conc. \emph{In Vivo} \tab TK Statistic Used* \tab Bioactive Chemical Conc. \emph{In Vitro} \cr
#'Honda1 \tab Veinous (Plasma) \tab Restrictive \tab Free \tab Mean Conc. In Vivo \tab Free Conc. In Vitro \cr
#'Honda2 \tab Veinous \tab Restrictive \tab Free \tab Mean Conc. In Vivo \tab Nominal Conc. In Vitro \cr
#'Honda3 \tab Veinous \tab Restrictive \tab Total \tab Mean Conc. In Vivo \tab Nominal Conc. In Vitro \cr
#'Honda4 \tab Target Tissue \tab Non-restrictive \tab Total \tab Mean Conc. In Vivo \tab Nominal Conc. In Vitro \cr
#'}
#'
#' "Honda1" uses plasma concentration, restrictive clearance, and treats the
#' unbound invivo concentration as bioactive. For IVIVE, any input nominal
#' concentration in vitro should be converted to cfree.invitro using
#' \code{\link{armitage_eval}}, otherwise performance will be the same as
#' "Honda2".
#'
#' @examples
#' honda.ivive(method = "Honda1", tissue = NULL)
#'
#' @author Greg Honda and John Wambaugh
#'
#' @keywords Solve
#'
#' @references
#' \insertRef{honda2019using}{httk}
#'
#' @export honda.ivive
#'
#'
honda.ivive <- function(method="Honda1",tissue="liver"){
#R CMD CHECK throws notes about "no visible binding for global variable", for
#each time a data.table column name is used without quotes. To appease R CMD
#CHECK, a variable has to be created for each of these column names and set to
#NULL. Note that within the data.table, these variables will not be NULL! Yes,
#this is pointless and annoying.
restrictive.clearance<-bioactive.free.invivo<-concentration<-NULL
#End R CMD CHECK appeasement.
if (is.null(tissue)) tissue <- "liver"
if (tolower(method)==tolower("Honda1"))
{
tissue <- NULL
restrictive.clearance <- T
bioactive.free.invivo <- T
concentration <- "plasma"
warning("Argument method =\"Honda1\" uses plasma concentration, restrictive clearance, and treats the unbound invivo concentration as bioactive.
For IVIVE, any input nominal concentration in vitro should be converted to cfree.invitro using armitage_eval(),
otherwise performance will be the same as \"Honda2\". Use show_honda.ivive() to print summary of Honda et al. 2019 results.")
} else if (tolower(method)==tolower("Honda2"))
{
tissue <- NULL
restrictive.clearance <- T
bioactive.free.invivo <- T
concentration <- "plasma"
warning("Argument method =\"Honda2\" uses plasma concentration, restrictive clearance, and treats the unbound concentration as bioactive.")
} else if (tolower(method)==tolower("Honda3"))
{
tissue <- NULL
restrictive.clearance <- T
bioactive.free.invivo <- F
concentration <- "plasma"
warning("Argument method =\"Honda3\" uses plasma concentration, restrictive clearance, and treats the total concentration as bioactive.
This is equivalent to the default httk assumptions.")
} else if (tolower(method)==tolower("Honda4"))
{
tissue <- tolower(tissue)
restrictive.clearance <- F
bioactive.free.invivo <- F
concentration <- "tissue"
warning(paste("Argument method =\"Honda4\" uses target tissue (",tissue,") concentration, non-restrictive clearance, and treats the total concentration as bioactive.",sep=""))
}else stop("Only four sets of IVIVE assumptions that performed well in Honda et al. (2019) are included: \"Honda1\" through \"Honda4\". The use of max (peak) concentration can not be currently be calculated with calc_analytic_css.")
return(list("tissue" = tissue,
"bioactive.free.invivo" = bioactive.free.invivo,
"restrictive.clearance" = restrictive.clearance,
"concentration" = concentration))
}
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