## ----setup, include=FALSE, eval = TRUE----------------------------------------
knitr::opts_chunk$set(echo = TRUE, fig.width=6, fig.height=5)

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

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

## ----InitialPrep, eval = execute.vignette-------------------------------------
# library(data.table)
# library(magrittr)
# library(ggplot2)
# library(httk)
# library(httkexamples)

## ----MakeTable, eval = execute.vignette---------------------------------------
# armitage.dt <- copy(armitage_input)
# armitage.dt[,well_number:=384] %>%
#   .[,option.bottom:=TRUE] %>%
#   .[,option.plastic:=TRUE] %>%
#   .[,Tsys:=37] %>%
#   .[,Tref:=298.15] %>%
#   .[,FBSf:=0.1] %>%
#   .[,nomconc:=50]
# 
# # Make sure we have data for the chemical:
# armitage.dt <- subset(armitage.dt,casrn%in%get_cheminfo(model="armitage"))
# # These chemicals are missing water solubilities:
# armitage.dt <- subset(armitage.dt,!(casrn%in%c("71751-41-2","34590-94-8","141517-21-7")))
# 
# armitage.dt2 <- armitage_estimate_sarea(tcdata = armitage.dt)
# armitage_output1 <- armitage_eval(tcdata = armitage.dt2[,ac50:=50])
# armitage_output2 <- armitage_eval(tcdata = armitage.dt2[,ac50:=1])
# armitage_output3 <- armitage_eval(tcdata = armitage.dt2[,ac50:=0.001])
# 

## ----MakePlot, echo=TRUE, eval = execute.vignette-----------------------------
# armitage_output <- rbind(armitage_output1[,xfill:="50 \U00B5M"],
#                          armitage_output2[,xfill:="1 \U00B5M"],
#                          armitage_output3[,xfill:="1 nM"])
# armitage_output[,xfill:=factor(xfill,levels=c("50 \U00B5M","1 \U00B5M","1 nM"))]
# 
# ggplot(armitage_output) +
#   geom_point(aes(x=gkow,y=log10(ccells/MW*1e9),color=xfill),shape=1) +
#   labs(color=expression("AC"["50"]),x="log P", y = "log(ng chemical/g cells)") +
#   theme_bw()