## ----knitrPrep, include=FALSE, eval = TRUE------------------------------------
knitr::opts_chunk$set(echo = TRUE, fig.width=5, fig.height=4)

## ----clear_memory, eval = TRUE------------------------------------------------
rm(list=ls()) 

## ----runchunks, eval = TRUE---------------------------------------------------
# Set whether or not the following chunks will be executed (run):
execute.vignette <- FALSE

## ----setup, eval = execute.vignette-------------------------------------------
#  library(httk)
#  library(ggplot2)
#  library(scales)

## ----scientific.notation, eval = execute.vignette-----------------------------
#  scientific_10 <- function(x) {
#    out <- gsub("1e", "10^", scientific_format()(x))
#    out <- gsub("\\+","",out)
#    out <- gsub("10\\^01","10",out)
#    out <- parse(text=gsub("10\\^00","1",out))
#  }

## ----Frank2018data, eval = execute.vignette-----------------------------------
#  chem.table <- Frank2018invivo

## ----ivive.loop, eval = execute.vignette--------------------------------------
#  for (this.row in 1:dim(chem.table)[1])
#  {
#    this.cas <- chem.table[this.row,"Substance_CASRN"]
#    if (tolower(chem.table[this.row,"Species"])=="rodent")
#    {
#      this.species <- "rat"
#    } else if (tolower(chem.table[this.row,"Species"])=="rat")
#    {
#      this.species <- "rat"
#    } else if (tolower(chem.table[this.row,"Species"])=="human")
#    {
#      this.species <- "human"
#    }
#    else if (tolower(chem.table[this.row,"Species"])=="mouse")
#    {
#      this.species <- "mouse"
#    }
#    else browser()
#    if (chem.table[this.row,"Route"] %in% c("i.p.","s.c.","i.m.")) iv.dose =TRUE
#    else if (chem.table[this.row,"Route"]=="oral") iv.dose = F
#    else browser()
#    this.dose <- chem.table[this.row,"Dose"]
#    this.days <- chem.table[this.row,"Days"]
#  # Make sure the dose units are in mg/kg body weight:
#    if (regexpr("ug",chem.table[this.row,"Dose.Units"])!=-1)
#    {
#      this.dose <- this.dose/1000
#    }
#    if (regexpr("/kg",chem.table[this.row,"Dose.Units"])==-1)
#    {
#      this.dose <- this.dose/0.25
#    }
#  # Here we run the HTTK PBPK Model:
#    out <- suppressWarnings(solve_pbtk(chem.cas=this.cas,
#             dose=this.dose,
#             species=this.species,
#  # This was used in 2017 but I don't agree with it anymore:
#  #           restrictive.clearance=FALSE,
#             days=this.days,
#             iv.dose=iv.dose,
#             default.to.human=TRUE))
#  
#  # Record the Cmax and the AUC:
#    chem.table[this.row,"Cmax"] <- max(out[,"Cplasma"])
#    chem.table[this.row,"AUC"] <- max(out[,"AUC"])
#  }

## ----Frank2018.Fig6, eval = execute.vignette----------------------------------
#  Fig.AUC <- ggplot(data=chem.table) +
#    geom_segment(color="grey",aes(x=AUC,y=Lower.95..CI,xend=AUC,yend=Higher.95..CI))+
#  #  geom_point(aes(x=AUC,y=Critical.concentration,color="Chemical"))+
#     geom_text(aes(x=AUC,y=Critical.concentration,label=Compound.abbrev,color=Chemical)) +
#     scale_y_log10(label=scientific_10,limits=c(10^-7,100)) +
#     scale_x_log10(label=scientific_10,limits=c(10^-7,100)) +
#      annotation_logticks() +
#      geom_abline(slope=1, intercept=0) +
#      geom_abline(slope=1, intercept=1,linetype="dashed") +
#      geom_abline(slope=1, intercept=-1,linetype="dashed") +
#      xlab(expression(paste(italic("In vivo")," AUC estimated with HTTK (uM*day)"))) +
#      ylab(expression(paste(italic("In vitro")," predicted Critical Conc. (uM)"))) +
#      scale_color_brewer(palette="Set2") +
#      theme_bw()  +
#      theme(legend.position="bottom")
#  
#  print(Fig.AUC)