## ----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

## ----load_libraries, eval=execute.vignette------------------------------------
# library(httk)
# library(gdata)
# library(ggplot2)
# library(viridis)
# library(censReg)
# library(gmodels)
# library(gplots)
# library(scales)
# library(colorspace)
# library(gridExtra)

## ----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))
# }

## ----setuppctable, eval=execute.vignette--------------------------------------
# pc.table <- NULL
# pc.data <- subset(pc.data,fu != 0 & Exp_PC != 0 & Tissue %in% c("Adipose","Bone","Brain","Gut",
#     "Heart","Kidney","Liver","Lung","Muscle","Skin","Spleen","Blood Cells") &
#     tolower(Species) == 'rat' & !CAS %in% c('10457-90-6','5786-21-0','17617-23-1','69-23-8','2898-12-6',
#     '57562-99-9','59-99-4','2955-38-6','155-97-5','41903-57-5','58-55-9','77-32-7','59-05-2','60-54-8'))
# cas.list <- get_cheminfo(model='schmitt',species='rat',suppress.messages=TRUE)
# cas.list <-  cas.list[cas.list %in% pc.data[,'CAS']]
# ma.data.list <- subset(chem.physical_and_invitro.data,!is.na(logMA))[,'CAS']
# for(this.cas in cas.list){
#   parameters <- parameterize_schmitt(
#     chem.cas=this.cas,
#     species='rat',
#     suppress.messages=TRUE)
#   init.parameters <- parameters
#   charge <- calc_ionization(
#     chem.cas=this.cas,
#     pH=7.4)$fraction_charged
#   if(!this.cas %in% ma.data.list){
#     init.parameters$MA <- 10^(0.999831 - 0.016578*38.7 + 0.881721 * log10(parameters$Pow))
#   }
#   pcs <- predict_partitioning_schmitt(
#     parameters=parameters,
#     species='rat',
#     regression=FALSE,
#     suppress.messages=TRUE
#     )
#   init.pcs <- predict_partitioning_schmitt(
#     parameters=init.parameters,
#     species='rat',
#     regression=FALSE,
#     suppress.messages=TRUE)
#   for(this.tissue in subset(pc.data,CAS==this.cas)[,'Tissue']){
#     if(this.tissue == 'Blood Cells') this.pc <- 'rbc'
#     else this.pc <- this.tissue
#         pc.table <- rbind(pc.table,
#                       cbind(
#                         as.data.frame(this.cas),
#                         as.data.frame(this.tissue),
#                         as.data.frame(log10(
#                           init.pcs[[which(substr(names(init.pcs),
#                             2,
#                             nchar(names(init.pcs))-3) ==
#                             tolower(this.pc))]] *
#                           init.parameters$Funbound.plasma)),
#                         as.data.frame(log10(
#                           pcs[[which(substr(names(pcs),
#                             2,
#                             nchar(names(pcs))-3) ==
#                             tolower(this.pc))]] *
#                           parameters$unadjusted.Funbound.plasma)),
#                         as.data.frame(log10(
#                           init.pcs[[which(substr(names(init.pcs),
#                             2,
#                             nchar(names(init.pcs))-3) ==
#                             tolower(this.pc))]] *
#                           init.parameters$unadjusted.Funbound.plasma)),
#                         as.data.frame(log10(
#                           pcs[[which(substr(names(pcs),
#                             2,
#                             nchar(names(pcs))-3) == tolower(this.pc))]] *
#                             parameters$Funbound.plasma)),
#                         as.data.frame(log10(
#                           subset(pc.data,
#                             CAS==this.cas & Tissue==this.tissue)[,'Exp_PC'])),
#                         as.data.frame(subset(pc.data,
#                           CAS==this.cas & Tissue==this.tissue)[,'LogP']),
#                         as.data.frame(charge),
#                         as.data.frame(as.character(subset(pc.data,
#                           CAS == this.cas)[1,'A.B.N'])),
#                         as.data.frame(subset(pc.data,
#                           CAS == this.cas)[1,'fu'])))
#   }
# }
# colnames(pc.table) <- c('CAS','Tissue',
#                         'fup.correction',
#                         'ma.correction',
#                         'init.Predicted',
#                         'Predicted',
#                         'Experimental',
#                         'logP',
#                         'charge',
#                         'type',
#                         'fup')
# init.error <- pc.table[,'Experimental'] - pc.table[,'init.Predicted']
# fup.error <- pc.table[,'Experimental'] - pc.table[,'fup.correction']
# ma.error <- pc.table[,'Experimental'] - pc.table[,'ma.correction']
# final.error <- pc.table[,'Experimental'] - pc.table[,'Predicted']
# fup.improvement <- abs(init.error) - abs(fup.error)
# ma.improvement <- abs(init.error) - abs(ma.error)
# final.improvement <- abs(init.error) - abs(final.error)
# pc.table <- cbind(pc.table,fup.improvement,ma.improvement, final.improvement,
#                   final.error,init.error,ma.error,fup.error)

## ----KpFigures, eval=execute.vignette-----------------------------------------
# init.plot <- ggplot() +
#   geom_point(data=pc.table,aes(10^(init.Predicted),10^(Experimental))) +
#   geom_abline() +
#   labs(y=expression(paste("Measured ",K[p])),
#        x=expression(paste("Predicted ",K[p]))) +
#   theme(axis.text=element_text(size=16),axis.title=element_text(size=16),
#     plot.title=element_text(size=18,hjust = 0.5)) +
#   scale_x_log10(label=scientific_10,limits=c(0.01,10^4.5)) +
#   scale_y_log10(label=scientific_10,limits=c(0.01,10^4.5)) +
#   ggtitle('(A)')
# print(init.plot)
# init.stats <- summary(lm(Experimental ~ init.Predicted,
#                          data=pc.table))
# 
# final.plot <- ggplot() +
#   geom_point(data=pc.table,aes(10^(Predicted),10^(Experimental))) +
#   geom_abline() +
#   labs(y=expression(paste("Measured ",K[p])),
#        x=expression(paste("Predicted ",K[p]))) +
#   theme(axis.text=element_text(size=16),axis.title=element_text(size=16),
#     plot.title=element_text(size=18,hjust=0.5)) +
#   scale_x_log10(label=scientific_10,limits=c(0.01,10^4.5)) +
#   scale_y_log10(label=scientific_10,limits=c(0.01,10^4.5)) +
#   ggtitle('(B)')
# print(final.plot)
# final.stats <- summary(lm(Experimental ~ Predicted,
#                           data=pc.table))
# 
# fup.change.plot <-  ggplot() +
#   geom_point(data=pc.table[order(pc.table[,'fup.improvement'],decreasing=F),],
#     aes(10^(fup.correction),10^(Experimental),color=fup.improvement)) +
#   geom_abline() +
#   labs(y=expression(paste("Measured ",K[p])),
#        x=expression(paste("Predicted ",K[p])),color='Improvement') +
#   theme(axis.text=element_text(size=16),axis.title=element_text(size=16)) +
#   scale_x_log10(label=scientific_10,limits=c(0.01,10^4.5)) +
#   scale_y_log10(label=scientific_10,limits=c(0.01,10^4.5)) +
#   scale_color_viridis(direction=-1,option='inferno')
# print(fup.change.plot)
# fup.stats <- summary(lm(Experimental ~ fup.correction,
#                      data=pc.table))
# 
# ma.subset <- subset(pc.table,!CAS %in% ma.data.list)
# ma.change.plot <- ggplot() +
#     geom_point(data=ma.subset[order(ma.subset[,'ma.improvement']
#       ,decreasing=F),],
#       aes(10^(ma.correction),10^(Experimental),color=ma.improvement)) +
#     geom_abline() +
#     labs(y=expression(paste("Measured ",K[p])),
#       x=expression(paste("Predicted ",K[p])),color='Improvement') +
#     theme(axis.text=element_text(size=16),axis.title=element_text(size=16)) +
#     scale_x_log10(label=scientific_10,limits=c(0.01,10^4.5)) +
#     scale_y_log10(label=scientific_10,limits=c(0.01,10^4.5)) +
#     scale_color_viridis(direction=-1,option='inferno')
# print(ma.change.plot)
# ma.stats <- summary(lm(Experimental ~ ma.correction,
#                     data=ma.subset))
# 
# fup.table <- data.frame(Test=c("Initial Tissue PC Accuracy","Fup Lipid Correction","Membrane Affinity","Final"),
#                            RSquared = signif(c(init.stats$adj.r.squared,
#                                          fup.stats$adj.r.squared,
#                                          ma.stats$adj.r.squared,
#                                          final.stats$adj.r.squared),3),
#                            RMSLE = signif(c(mean(init.stats$residuals^2,na.rm=TRUE)^(1/2),
#                                      mean(fup.stats$residuals^2,na.rm=TRUE)^(1/2),
#                                      mean(ma.stats$residuals^2,na.rm=TRUE)^(1/2),
#                                      mean(final.stats$residuals^2,na.rm=TRUE)^(1/2)),3)
#                           )
# knitr::kable(fup.table)

## ----performPCregressions, eval=execute.vignette------------------------------
# regressions <- NULL
# 
# for(tissue in as.character(unique(pc.table[,'Tissue']))){
#   fit <- lm(Experimental ~ Predicted ,data=subset(pc.table,Tissue==tissue))
#   smry <- summary(fit)
#   est <- estimable(fit, cm=diag(2), beta0=c(0,1), joint.test=TRUE)
#   regressions <- rbind(regressions,cbind(tissue,as.data.frame(fit$coefficients[['(Intercept)']]),
#       as.data.frame(fit$coefficients[['Predicted']]),
#       as.data.frame(smry$coefficients[['Predicted','Pr(>|t|)']]),
#       as.data.frame(smry$sigma),as.data.frame(smry$r.squared),
#       as.data.frame(smry[[11]][1,1]),as.data.frame(smry[[11]][2,2]),
#       as.data.frame(smry[[11]][1,2]),as.data.frame(smry$df[2]),as.data.frame(est[[3]])))
# }
# colnames(regressions) <- c('Tissue','Intercept','Slope','P-value','SE','R-squared',
#                            'Int Var','Slp Var','Cov','df','estimable')
# 
# for (this.col in 2:10) regressions[,this.col] <- signif(regressions[,this.col], 3)
# regressions <- regressions[order(regressions[,1]),]
# 
# knitr::kable(regressions, caption = "Table 1: The regressions for each tissue, after fup and membrane affinity adjustments, of the log10-transformed measured Kp regressed on
# predicted Kp")
# 
# write.table(regressions,
#             file=paste0("Pearce2017PCCalibration=",Sys.Date(),".txt"),
#             sep="/t",
#             row.names=FALSE)

## ----PCRegressionFigure, eval=execute.vignette--------------------------------
# x.cf <- seq(-2,3.5,.01)
# for(tissue in  as.character(unique(pc.table[,'Tissue'])))
# {
#   conf <- qt(0.975,df=subset(regressions,Tissue==tissue)[['df']]+1) *
#       subset(regressions,Tissue==tissue)[['SE']] *
#       sqrt(subset(regressions,Tissue==tissue)[['Int Var']] +
#       x.cf^2 * subset(regressions,Tissue==tissue)[['Slp Var']] +
#       2 * x.cf * subset(regressions,Tissue==tissue)[['Cov']] + 1)
#   line <- subset(regressions,Tissue==tissue)[['Intercept']] +
#       x.cf * subset(regressions,Tissue==tissue)[['Slope']]
#   y.cf <- line + conf
#   y.ncf <- line - conf
# 
#   cf <- cbind(as.data.frame(x.cf),as.data.frame(y.cf),as.data.frame(y.ncf))
#   if(tissue == 'Blood Cells'){
#     eval(parse(text= paste('Blood <- ggplot() +
#                                geom_abline(linetype = "dashed") +
#                                geom_point(data=subset(pc.table,Tissue == \'',tissue,'\'),aes(10^(Predicted),
#                                10^(Experimental)))  +  theme(axis.text=element_text(size=14),
#                                axis.title=element_text(size=14),plot.title=element_text(size=14)) +
#                                scale_x_log10(label=scientific_10,limits=c(0.01,1000)) +
#                                scale_y_log10(label=scientific_10,limits=c(0.01,1000)) +
#                                ylab(ifelse(tissue=="Brain",expression(paste("Inferred ",K[p])),"")) +
#                                xlab(ifelse(tissue=="Skin", expression(paste("Predicted ",K[p])),"")) +
#                                geom_line(data=cf,aes(10^(x.cf),10^(y.cf))) +
#                                geom_line(data=cf,aes(10^(x.cf),10^(y.ncf))) +
#                                geom_abline(intercept=subset(regressions,Tissue==tissue)[[\'Intercept\']],
#                                slope=subset(regressions,Tissue==tissue)[[\'Slope\']]) +
#                                ggtitle(\'Red Blood Cells\')',sep='')))
#   }else{
#     eval(parse(text= paste(tissue,' <- ggplot() + labs(y=expression(paste("Measured ",K[p]))
#                                ,x=expression(paste("Predicted ",K[p]))) + geom_abline(linetype = "dashed") +
#                                geom_point(data=subset(pc.table,Tissue == \'',tissue,'\'),
#                                aes(10^(Predicted),10^(Experimental))) + theme(axis.text=element_text(size=14),
#                                axis.title=element_text(size=14),plot.title=element_text(size=14)) +
#                                scale_x_log10(label=scientific_10,limits=c(0.01,1000)) +
#                                scale_y_log10(label=scientific_10,limits=c(0.01,1000)) +
#                                ylab(ifelse(tissue=="Brain",expression(paste("Inferred ",K[p])),"")) +
#                                xlab(ifelse(tissue=="Skin", expression(paste("Predicted ",K[p])),"")) +
#                                geom_line(data=cf,aes(10^(x.cf),10^(y.cf))) +
#                                geom_line(data=cf,aes(10^(x.cf),10^(y.ncf))) +
#                                geom_abline(intercept=subset(regressions,Tissue==tissue)[[\'Intercept\']],
#                                slope=subset(regressions,Tissue==tissue)[[\'Slope\']]) +
#                                ggtitle(\'',tissue,'\')',sep='')))
#   }
# }
# 
# grid.arrange(Adipose, Blood, Bone, Brain, Gut, Heart, Kidney, Liver, Lung, Muscle, Skin, Spleen, nrow=4)

## ----Vdevalaution, eval=execute.vignette--------------------------------------
# obach <- subset(Obach2008,CAS %in% get_cheminfo(model='schmitt'))
# vd.table <- NULL
# 
# for(this.cas in obach[,'CAS']){
#   parameters <- parameterize_schmitt(
#     chem.cas=this.cas,
#     suppress.messages=TRUE)
#   init.parameters <- parameters
#   if(!this.cas %in% ma.data.list){
#     init.parameters$MA <- 10^(0.999831 - 0.016578*37 + 0.881721 * log10(parameters$Pow))
#   }
#   pcs <- predict_partitioning_schmitt(
#     parameters=parameters,
#     regression=FALSE,
#     suppress.messages=TRUE)
#   init.pcs <- predict_partitioning_schmitt(
#     parameters=init.parameters,
#     regression=FALSE,
#     suppress.messages=TRUE)
#   reg.pcs <- predict_partitioning_schmitt(
#     parameters=parameters,
#     regression=TRUE,
#     suppress.messages=TRUE)
#   vdist <- calc_vdist(
#     parameters=c(pcs,Funbound.plasma=parameters$Funbound.plasma),
#     suppress.messages=TRUE)
#   init.vdist <- calc_vdist(
#     parameters=c(
#       init.pcs,
#       Funbound.plasma=parameters$unadjusted.Funbound.plasma),
#     suppress.messages = TRUE)
#   reg.vdist <- calc_vdist(
#     parameters=c(reg.pcs,Funbound.plasma=parameters$Funbound.plasma),
#     suppress.messages = TRUE)
#   vd.table <- rbind(
#     vd.table,
#     cbind(as.data.frame(this.cas),as.data.frame(log10(init.vdist)),
#     as.data.frame(log10(vdist)),as.data.frame(log10(reg.vdist)),
#     as.data.frame(log10(subset(obach,CAS==this.cas)[['VDss (L/kg)']]))))
# }
# colnames(vd.table) <- c(
#   'CAS',
#   'init.vdist',
#   'corrected.vdist',
#   'calibrated.vdist',
#   'Experimental')
# init.error <- vd.table[,'Experimental'] - vd.table[,'init.vdist']
# correction.error <- vd.table[,'Experimental'] - vd.table[,'corrected.vdist']
# calibration.error <- vd.table[,'Experimental'] - vd.table[,'calibrated.vdist']
# correction.improvement <- abs(init.error) - abs(correction.error)
# calibration.improvement <- abs(correction.error) - abs(calibration.error)
# vd.table <- cbind(vd.table,correction.improvement,calibration.improvement,
#                   init.error,correction.error,calibration.error)

## ----VdistRegressions, eval=execute.vignette----------------------------------
# fit <- lm(Experimental ~ calibrated.vdist,data=vd.table)
# smry <- summary(fit)
# calibrated.reg <- cbind(as.data.frame(fit$coefficients['(Intercept)']),
#                         as.data.frame(fit$coefficients['calibrated.vdist']),
#                         as.data.frame(smry$coefficients['calibrated.vdist','Pr(>|t|)']),
#                         as.data.frame(smry$sigma),as.data.frame(smry$r.squared))
# fit <- lm(Experimental ~ init.vdist,data=vd.table)
# smry <- summary(fit)
# init.reg <- cbind(as.data.frame(fit$coefficients['(Intercept)']),
#                   as.data.frame(fit$coefficients['init.vdist']),
#                   as.data.frame(smry$coefficients['init.vdist','Pr(>|t|)']),
#                   as.data.frame(smry$sigma),as.data.frame(smry$r.squared))
# fit <- lm(Experimental ~ corrected.vdist,data=vd.table)
# smry <- summary(fit)
# corrected.reg <- cbind(as.data.frame(fit$coefficients['(Intercept)']),
#                        as.data.frame(fit$coefficients['corrected.vdist']),
#                        as.data.frame(smry$coefficients['corrected.vdist','Pr(>|t|)']),
#                        as.data.frame(smry$sigma),as.data.frame(smry$r.squared))
# colnames(init.reg) <- colnames(corrected.reg) <-
# colnames(calibrated.reg) <- c('Intercept','Slope','P-value','Std Err','R-squared')

## ----VdistPlots, eval=execute.vignette----------------------------------------
# init.vd.plot <- ggplot(vd.table,aes(10^(init.vdist),10^(Experimental))) + geom_point() +
#     geom_abline(intercept = init.reg[['Intercept']], slope = init.reg[["Slope"]]) +
#     geom_abline(linetype = "dashed") + xlab("Predicted Volume of Distribution") +
#     ylab("Measured Volume of Distribution") + theme(axis.text=element_text(size=16),
#     axis.title=element_text(size=16),plot.title=element_text(size=18,hjust = 0.5)) +
#     scale_x_log10(label=scientific_10,limits=c(10^(-1.5),10^(8.5))) +
#     scale_y_log10(label=scientific_10,limits=c(10^(-1.5),10^(8.5))) +
#     ggtitle('(A)')
# print(init.vd.plot)
# 
# correction.plot <- ggplot() +
#     geom_point(data=vd.table[order(vd.table[,'correction.improvement'],decreasing=F),],
#     aes(10^(corrected.vdist),10^(Experimental),color=correction.improvement)) +
#     geom_abline(intercept = corrected.reg[['Intercept']],slope = corrected.reg[["Slope"]]) +
#     geom_abline(linetype = "dashed") + xlab("Predicted Volume of Distribution") +
#     ylab("Measured Volume of Distribution") + theme(legend.position = c(.95, .95),
#     legend.justification = c("right", "top"),legend.box.just = "right",
#     legend.margin = margin(6, 6, 6, 6),axis.text=element_text(size=16),
#     axis.title=element_text(size=16),plot.title=element_text(size=18,hjust = 0.5)) +
#     scale_x_log10(limits=c(10^(-1.5),10^(3))) + scale_y_log10(limits=c(10^(-1.5),10^(3))) +
#     ggtitle('(B)') + scale_color_viridis(direction=-1,option='inferno')
# print(correction.plot)
# 
# calibration.plot <- ggplot() +
#     geom_point(data=vd.table[order(vd.table[,'calibration.improvement'],decreasing=F),],
#     aes(10^(calibrated.vdist),10^(Experimental),color=calibration.improvement)) +
#     geom_abline(intercept = calibrated.reg[['Intercept']],slope = calibrated.reg[["Slope"]]) +
#     geom_abline(linetype = "dashed") + xlab("Predicted Volume of Distribution") +
#     ylab("Measured Volume of Distribution") + theme(legend.position = c(.95, .95),
#     legend.justification = c("right", "top"),legend.box.just = "right",
#     legend.margin = margin(6, 6, 6, 6),axis.text=element_text(size=16),
#     axis.title=element_text(size=16),plot.title=element_text(size=18,hjust = 0.5)) +
#     scale_x_log10(limits=c(10^(-1.5),10^(3))) + scale_y_log10(limits=c(10^(-1.5),10^(3))) +
#     ggtitle('(C)') + scale_color_viridis(direction=-1,option='inferno')
# print(calibration.plot)

## ----bloodtoplasmaevaluation, eval=execute.vignette---------------------------
# rb2p.data <- subset(chem.physical_and_invitro.data,!is.na(Human.Rblood2plasma))
# measured.rb2p <- NULL
# measured.krbc <- NULL
# predicted.rb2p <- NULL
# predicted.krbc <- NULL
# cas <- NULL
# charge <- NULL
# fup <- NULL
# logP <- NULL
# pka_donor <- NULL
# pka_accept <- NULL
# for(this.cas in rb2p.data[rb2p.data[,'CAS'] %in%
#   get_cheminfo(model='schmitt', suppress.messages = TRUE),'CAS'])
# {
#   rb2p <- get_rblood2plasma(chem.cas=this.cas)
#   krbc <- (rb2p + .44 - 1) / 0.44
#   measured.rb2p <- c(measured.rb2p,rb2p)
#   measured.krbc <- c(measured.krbc,krbc)
#   parameters <- parameterize_schmitt(
#     chem.cas=this.cas,
#     suppress.messages = TRUE)
#   pcs <- predict_partitioning_schmitt(
#     parameters=parameters,
#     suppress.messages=TRUE)
#   predicted.krbc <- c(predicted.krbc,pcs[['Krbc2pu']] * parameters$Funbound.plasma)
#   cas <- c(cas,this.cas)
#   charge <- c(charge,calc_ionization(chem.cas=this.cas,pH=7.4)$fraction_charged)
#   fup <- c(fup,parameters$unadjusted.Funbound.plasma)
#   logP <-  c(logP,log10(parameters$Pow))
#   pka_donor <- c(pka_donor,paste(parameters$pKa_Donor,collapse=','))
#   pka_accept <- c(pka_accept,paste(parameters$pKa_Accept,collapse=','))
# }
# predicted.rb2p <-  1 - 0.44 + 0.44 * predicted.krbc
# rb2p.table <- cbind(as.data.frame(cas),as.data.frame(predicted.rb2p),as.data.frame(measured.rb2p))
# colnames(rb2p.table) <- c('cas','predicted.rb2p','measured.rb2p')
# error <- log10(rb2p.table[,'measured.rb2p']) - log10(rb2p.table[,'predicted.rb2p'])
# rb2p.table <- cbind(rb2p.table,error,charge,fup,logP)
# 
# error <- log10(measured.krbc) -  log10(predicted.krbc)
# krbc.table <- cbind(as.data.frame(cas),as.data.frame(predicted.krbc),as.data.frame(measured.krbc),
#                     as.data.frame(error),charge,fup,logP,pka_donor,pka_accept)

## ----RBCStats, eval=execute.vignette------------------------------------------
# pdta <- data.frame(x = predicted.krbc,
#                    y = measured.krbc)
# pdta$y[pdta$y <= 0.1] <- 0.1
# pdta$Censoring <- factor(c("Not Censored","Censored")[as.numeric(pdta$y <= 0.1) + 1])
# y <- measured.krbc
# x <- cbind(rep(1, length(y)),-1 * log10(predicted.krbc))
# colnames(x) <- c("Intercept","Predicted")
# cc <- as.numeric(y <= 0.1)
# y[y < 0.1] <- 0.1
# y <- -log10(y)
# 
# out <- censReg(y~x, data = pdta, left=0.1)
# out$betas <- out$estimate

## ----RBCFigure, eval=execute.vignette-----------------------------------------
# censored.regression <- ggplot() +
#     geom_point(data=pdta,aes(x=x,y=y, color=Censoring)) +
#     scale_x_log10(limits=c(.0009,40)) + scale_y_log10(limits=c(.1,4),breaks=c(.1,.5,2.5)) +
#     labs(y=expression(paste("Inferred ",K[p])),x=expression(paste("Predicted ",K[p]))) +
#     geom_abline(intercept=0, slope=1, linetype='dashed') +
#     theme(axis.text=element_text(size=16),axis.title=element_text(size=16),
#     plot.title=element_text(size=18,hjust=0.5),legend.position = c(0.11, .8)) +
#     geom_abline(slope=out$betas[2],intercept=-out$betas[1]) + ggtitle('(B)')
# print(censored.regression)
# 
# rb2p.plot <- ggplot(rb2p.table,aes(predicted.rb2p,measured.rb2p)) +
#     geom_point()  + scale_x_log10(lim=c(.52,18)) +
#     scale_y_log10(lim=c(.52,2.5),breaks=c(0.5,1,2)) + geom_abline(linetype='dashed') +
#     labs(y=expression(paste("Measured Whole Blood ",K[p])),
#     x=expression(paste("Predicted Whole Blood ",K[p]))) +
#     theme(axis.text=element_text(size=16),axis.title=element_text(size=16),
#     plot.title=element_text(size=18,hjust=0.5)) + ggtitle('(A)')
# print(rb2p.plot)

## ----summarytable, eval=execute.vignette--------------------------------------
# heatmap.table <- NULL
# for(this.cas in get_cheminfo(model='schmitt')){
#     parms <- parameterize_schmitt(
#       chem.cas=this.cas,
#       suppress.messages = TRUE)
#     pcs <- predict_partitioning_schmitt(
#       parameters=parms,
#       suppress.messages = TRUE)
#     heatmap.table <- cbind(heatmap.table,log10(unlist(pcs)[1:11]*parms$Funbound.plasma))
# }
# rownames(heatmap.table) <-  c('Adipose','Bone','Brain','Gut','Heart',
#                               'Kidney','Liver','Lung','Muscle','Skin','Spleen')
# colnames(heatmap.table) <- rep("",dim(heatmap.table)[2])

## ----summaryheatmap, eval=execute.vignette------------------------------------
# pal <- function (n, h = c(260, -328), c = 80, l = c(30, 100), power = 1.5,
#     fixup = TRUE, gamma = NULL, alpha = 1, ...)
# {
#     if (!is.null(gamma))
#         warning("'gamma' is deprecated and has no effect")
#     if (n < 1L)
#         return(character(0L))
#    h <- rep(h, length.out = 2L)
#     c <- c[1L]
#     l <- rep(l, length.out = 2L)
#     power <- rep(power, length.out = 2L)
#     rval <- seq(1, -1, length = n)
#     rval <- hex(polarLUV(L = l[2L] - diff(l) * abs(rval)^power[2L],
#         C = c * abs(rval)^power[1L], H = ifelse(rval > 0, h[1L],
#             h[2L])), fixup = fixup, ...)
#     if (!missing(alpha)) {
#         alpha <- pmax(pmin(alpha, 1), 0)
#         alpha <- format(as.hexmode(round(alpha * 255 + 1e-04)),
#             width = 2L, upper.case = TRUE)
#         rval <- paste(rval, alpha, sep = "")
#     }
#     return(rval)
# }
# 
# hclust.ave <- function(x) hclust(x, method="ward.D2")
# heatmap.2(heatmap.table,col=pal,trace="none", hclustfun=hclust.ave,
#           key.xlab=expression(paste("log10 ",K[p]," Value")),
#           key.ylab=expression(paste("Number of ",K[p])),
#           key.title="Partition Coefficient",xlab="Chemicals",cex.lab=2,margins=c(2,5))

