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#' Get literature Css
#'
#' This function retrieves a steady-state plasma concentration as a result of
#' infusion dosing from the Wetmore et al. (2012) and (2013) publications and
#' other literature.
#'
#' @param chem.name Either the chemical name or the CAS number must be
#' specified.
#' @param chem.cas Either the cas number or the chemical name must be
#' specified.
#' @param which.quantile Which quantile from the SimCYP Monte Carlo simulation
#' is requested. Can be a vector.
#' @param species Species desired (either "Rat" or default "Human").
#' @param clearance.assay.conc Concentration of chemical used in measureing
#' intrinsic clearance data, 1 or 10 uM.
#' @param daily.dose Total daily dose infused in units of mg/kg BW/day.
#' Defaults to 1 mg/kg/day.
#' @param output.units Returned units for function, defaults to mg/L but can
#' also be uM (specify units = "uM").
#' @param suppress.messages Whether or not the output message is suppressed.
#'
#' @return A numeric vector with the literature steady-state plasma
#' concentration (1 mg/kg/day) for the requested quantiles
#'
#' @author John Wambaugh
#'
#' @references Wetmore, B.A., Wambaugh, J.F., Ferguson, S.S., Sochaski, M.A.,
#' Rotroff, D.M., Freeman, K., Clewell, H.J., Dix, D.H., Andersen, M.E., Houck,
#' K.A., Allen, B., Judson, R.S., Sing, R., Kavlock, R.J., Richard, A.M., and
#' Thomas, R.S., "Integration of Dosimetry, Exposure and High-Throughput
#' Screening Data in Chemical Toxicity Assessment," Toxicological Sciences 125
#' 157-174 (2012)
#'
#' Wetmore, B.A., Wambaugh, J.F., Ferguson, S.S., Li, L., Clewell, H.J. III,
#' Judson, R.S., Freeman, K., Bao, W, Sochaski, M.A., Chu T.-M., Black, M.B.,
#' Healy, E, Allen, B., Andersen M.E., Wolfinger, R.D., and Thomas R.S., "The
#' Relative Impact of Incorporating Pharmacokinetics on Predicting in vivo
#' Hazard and Mode-of-Action from High-Throughput in vitro Toxicity Assays"
#' Toxicological Sciences, 132:327-346 (2013).
#'
#' Wetmore, B. A., Wambaugh, J. F., Allen, B., Ferguson, S. S., Sochaski, M.
#' A., Setzer, R. W., Houck, K. A., Strope, C. L., Cantwell, K., Judson, R. S.,
#' LeCluyse, E., Clewell, H.J. III, Thomas, R.S., and Andersen, M. E. (2015).
#' "Incorporating High-Throughput Exposure Predictions with Dosimetry-Adjusted
#' In Vitro Bioactivity to Inform Chemical Toxicity Testing" Toxicological
#' Sciences, kfv171.
#'
#' @keywords Literature Monte-Carlo
#'
#' @examples
#' get_lit_css(chem.cas="34256-82-1")
#'
#' get_lit_css(chem.cas="34256-82-1",species="Rat",which.quantile=0.5)
#'
#' get_lit_css(chem.cas="80-05-7", daily.dose = 1,which.quantile = 0.5, output.units = "uM")
#'
#' @export get_lit_css
get_lit_css <- function(
chem.cas=NULL,
chem.name=NULL,
daily.dose=1,
which.quantile=0.95,
species="Human",
clearance.assay.conc=NULL,
output.units="mg/L",
suppress.messages=FALSE)
{
Wetmore.data <- Wetmore.data
if (species == "Human") available.quantiles <- c(0.05,0.5, 0.95)
else available.quantiles <- 0.5
if (!all(which.quantile %in% available.quantiles)) stop(
"Literature only includes 5%, 50%, and 95% quantiles for human and 50% for rat.")
if (!(tolower(output.units) %in% c("mg/l","um"))) stop(
"Literature only includes mg/L and uM values for Css")
out <- get_chem_id(chem.cas=chem.cas,chem.name=chem.name)
chem.cas <- out$chem.cas
chem.name <- out$chem.name
this.data <- subset(Wetmore.data,Wetmore.data[,"CAS"] == chem.cas &
toupper(Wetmore.data[,"Species"])==toupper(species))
if (!is.null(clearance.assay.conc))
{
this.data <- subset(this.data,this.data[,"Concentration..uM."] ==
clearance.assay.conc)[1,]
if (dim(this.data)[1]!=1) stop(
paste("No",
clearance.assay.conc,
"uM clearance assay data for",
chem.name,
"in",
species))
}else{
if (1 %in% this.data[,"Concentration..uM."]) {
this.data <- subset(this.data,this.data[,"Concentration..uM."]== 1)[1,]
clearance.assay.conc <- 1
} else {
this.data <- this.data[1,]
clearance.assay.conc <- this.data[,"Concentration..uM."][[1]]
}
}
out <- NULL
if (tolower(output.units)=="mg/l")
{
if (0.05 %in% which.quantile) out <-
c(out,daily.dose*this.data[,"Css_lower_5th_perc.mg.L."])
if (0.5 %in% which.quantile) out <-
c(out,daily.dose*this.data[,"Css_median_perc.mg.L."])
if (0.95 %in% which.quantile) out <-
c(out,daily.dose*this.data[,"Css_upper_95th_perc.mg.L."])
} else if(tolower(output.units) == 'um') {
if (0.05 %in% which.quantile) out <-
c(out,daily.dose*this.data[,"Css_lower_5th_perc.uM."])
if (0.5 %in% which.quantile) out <-
c(out,daily.dose*this.data[,"Css_median_perc.uM."])
if (0.95 %in% which.quantile) out <-
c(out,daily.dose*this.data[,"Css_upper_95th_perc.uM."])
} else{
stop('Output.units can only be uM or mg/L.')
}
if (!suppress.messages) {
cat(paste(
toupper(substr(species,1,1)),
substr(species,2,nchar(species)),
" plasma concentrations returned in ",
output.units,
" units.\n",
sep=""))
cat(paste(
"Retrieving Css from literature based on ",
clearance.assay.conc,
" uM intrinsic clearance data for the ",
which.quantile,
" quantile in ",
species,
".\n",
sep=""))
}
return(set_httk_precision(out))
}
#' Get literature Css (deprecated).
#'
#' This function is included for backward compatibility. It calls
#' \code{\link{get_lit_css}} which
#' retrieves a steady-state plasma concentration as a result of
#' infusion dosing from the Wetmore et al. (2012) and (2013) publications and
#' other literature.
#'
#' @param chem.name Either the chemical name or the CAS number must be
#' specified.
#' @param chem.cas Either the cas number or the chemical name must be
#' specified.
#' @param which.quantile Which quantile from the SimCYP Monte Carlo simulation
#' is requested. Can be a vector.
#' @param species Species desired (either "Rat" or default "Human").
#' @param clearance.assay.conc Concentration of chemical used in measureing
#' intrinsic clearance data, 1 or 10 uM.
#' @param daily.dose Total daily dose infused in units of mg/kg BW/day.
#' Defaults to 1 mg/kg/day.
#' @param output.units Returned units for function, defaults to mg/L but can
#' also be uM (specify units = "uM").
#' @param suppress.messages Whether or not the output message is suppressed.
#'
#' @return A numeric vector with the literature steady-state plasma
#' concentration (1 mg/kg/day) for the requested quantiles
#'
#' @author John Wambaugh
#'
#' @references Wetmore, B.A., Wambaugh, J.F., Ferguson, S.S., Sochaski, M.A.,
#' Rotroff, D.M., Freeman, K., Clewell, H.J., Dix, D.H., Andersen, M.E., Houck,
#' K.A., Allen, B., Judson, R.S., Sing, R., Kavlock, R.J., Richard, A.M., and
#' Thomas, R.S., "Integration of Dosimetry, Exposure and High-Throughput
#' Screening Data in Chemical Toxicity Assessment," Toxicological Sciences 125
#' 157-174 (2012)
#'
#' Wetmore, B.A., Wambaugh, J.F., Ferguson, S.S., Li, L., Clewell, H.J. III,
#' Judson, R.S., Freeman, K., Bao, W, Sochaski, M.A., Chu T.-M., Black, M.B.,
#' Healy, E, Allen, B., Andersen M.E., Wolfinger, R.D., and Thomas R.S., "The
#' Relative Impact of Incorporating Pharmacokinetics on Predicting in vivo
#' Hazard and Mode-of-Action from High-Throughput in vitro Toxicity Assays"
#' Toxicological Sciences, 132:327-346 (2013).
#'
#' Wetmore, B. A., Wambaugh, J. F., Allen, B., Ferguson, S. S., Sochaski, M.
#' A., Setzer, R. W., Houck, K. A., Strope, C. L., Cantwell, K., Judson, R. S.,
#' LeCluyse, E., Clewell, H.J. III, Thomas, R.S., and Andersen, M. E. (2015).
#' "Incorporating High-Throughput Exposure Predictions with Dosimetry-Adjusted
#' In Vitro Bioactivity to Inform Chemical Toxicity Testing" Toxicological
#' Sciences, kfv171.
#'
#' @keywords Literature Monte-Carlo
#'
#' @examples
#' get_lit_css(chem.cas="34256-82-1")
#'
#' get_lit_css(chem.cas="34256-82-1",species="Rat",which.quantile=0.5)
#'
#' get_lit_css(chem.cas="80-05-7", daily.dose = 1,which.quantile = 0.5, output.units = "uM")
#
#' @export get_wetmore_css
get_wetmore_css <- function(
chem.cas=NULL,
chem.name=NULL,
daily.dose=1,
which.quantile=0.95,
species="Human",
clearance.assay.conc=NULL,
output.units="mg/L",
suppress.messages=FALSE)
{
if (!suppress.messages)
warning("Function \"get_wetmore_css\" has been renamed to \"get_lit_cheminfo\".")
return(do.call(get_lit_css, args=purrr::compact(list(
chem.cas=chem.cas,
chem.name=chem.name,
daily.dose=daily.dose,
which.quantile=which.quantile,
species=species,
clearance.assay.conc=clearance.assay.conc,
output.units=output.units,
suppress.messages=suppress.messages))))
}
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