---
title: "Wambaugh et al. (2018): Estimating TK Parameters from In Vivo Data"
author: "John Wambaugh and Caroline Ring"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Wambaugh et al. (2018): Estimating TK Parameters from In Vivo Data}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include=FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = '#>')
```
To use the code in this vignette, you'll first need to load a few packages (if you haven't already).
```{r load_packages, eval = FALSE}
library(invivoPKfit)
```
# Initialized the Random Number Generator:
```{R initialize, eval = FALSE}
TeachingDemos::char2seed("Caroline Ring")
```
# Do the noncompartment model fit
```{r noncomp, eval=FALSE}
system.time(PK.fit.table.noncomp <- invivoPKfit::fit_all(data.set=pkdataset_nheerlcleaned, model="noncompartment"))

saveRDS(PK.fit.table.noncomp , paste("output/PK_fit_table_noncomp-",Sys.Date(),".rda",sep=""))
```
# Do the 2-compartment model fit
```{r twocomp, eval=FALSE}
system.time(PK.fit.table.2comp  <- invivoPKfit::fit_all(pkdataset_nheerlcleaned, model="2compartment", modelfun="analytic"))

saveRDS(PK.fit.table.2comp, paste("output/PK_fit_table_2comp-",Sys.Date(),".rda",sep=""))
```
# Plot the 2-compartment concentration vs. time
```{r twcomp_plot, eval=FALSE}
junk <- plot_conctime(PK.fit.table=PK.fit.table.2comp,
                      data.set=pkdataset_nheerlcleaned,
                      model="2compartment")
```
# Do the 1-compartment model fit
```{r onecomp, eval=FALSE}
system.time(PK.fit.table.1comp <- invivoPKfit::fit_all(data.set=pkdataset_nheerlcleaned, model="1compartment", modelfun="analytic"))

saveRDS(PK.fit.table.1comp, paste("output/PK_fit_table_1comp-",Sys.Date(),".rda",sep=""))
```
# Plot one compartment concentration vs. time
```{r onecomp_plot,eval=FALSE}
junk <- plot_conctime(PK.fit.table=PK.fit.table.1comp,
                      data.set=pkdataset_nheerlcleaned,
                      model="1compartment")
```
# Output the dataset analyzed:
```{r dataoutput,eval=FALSE}
write.csv(pkdataset_nheerlcleaned[order(pkdataset_nheerlcleaned$Compound),],"SupTable1.txt",row.names=F)
write.csv(pkdataset_nheerlcleaned[order(pkdataset_nheerlcleaned$Compound),],file=paste("InVivoData-",Sys.Date(),".txt",sep=""),row.names=F)
save(pkdataset_nheerlcleaned,file=paste("PKdata-",Sys.Date(),".RData",sep=""))
```