20-workshop.txt

---
title: NONMEM workshop 2018
author: Sungpil Han, Kyun-Seop Bae
date: 2017-02-22
bibliography: bibliography.bib
output:
  html_document:
    toc: yes
    keep_md: yes
  word_document:
    toc: yes
  pdf_document:
    includes:
      in_header: preamble.tex
editor_options: 
  chunk_output_type: console
---

```{r include = FALSE}
knitr::read_chunk("c.R")
```

```{r IndependentChunk, include = FALSE}
```

```{r include = FALSE}
## input_tidy --------------------------------------------------------------
#NMDataset = Emax
#Method = ZERO
#nTheta = 2
#nEta = 1
#nEps = 1
#THETAinit = 10,100
#OMinit = 0.2
#SGinit = 1

inputFirst <- read.csv("result/inputFirst.csv", as.is = TRUE, row.names = 1)
input <- data.frame(t(inputFirst), stringsAsFactors = FALSE)
NMDataset <- input$Dataset
METHOD <- input$Method 
nTheta <- as.numeric(input$nTheta)
nEta <- as.numeric(input$nEta)
nEps <- as.numeric(input$nEps)
THETAinit <- as.numeric(unlist(strsplit(input$THETAinit, split=",")))
OMinit <- matrix(as.numeric(unlist(strsplit(input$OMinit, split=","))), nrow=nEta, ncol=nEta)
SGinit <- matrix(as.numeric(unlist(strsplit(input$SGinit, split=","))), nrow=nEps, ncol=nEps)

LB = rep(0, nTheta)
UB = rep(1000000, nTheta)

if (length(intersect(dir(), "result")) == 0) {
    system("mkdir result")
}

system("cp cover.jpg result")
```

![Cover](cover.jpg)



<https://github.com/asancpt/nmw2017edison>
license: GPL-3

## Introduction

NONMEM Workshop 2017에서 사용된 nmw 패키지를 사용한 Edison 사이언스 앱입니다. [@Kim_2015;@Bae_2016;@Bae_2017]

## Result

A table (head) and a figure of input dataset is shown below.

### Initial values

```{r}
kable(inputFirst, format = "markdown")
```

### Input Table

```{r include = FALSE}
enableJIT(3)
##setwd("C:/NMW2017/03-Emax")

if (NMDataset == "Emax"){
    DataFile <- "03-Emax/SimData.CSV"
    DataAll <- read.csv(DataFile)
} else if (NMDataset == "Theoph") {
    Theo = Theoph[,c("Subject", "Time", "conc")]
    colnames(Theo) = c("ID" ,"TIME", "DV")
    DataAll <- Theo
}
```

```{r}
kable(head(DataAll, n = 20), caption = "input data", format = "markdown")
```

### Figure

```{r include = FALSE}
pdf("result/xyplot.pdf")
if (NMDataset == "Emax") xyplot(DV ~ log(CE) | ID, data=DataAll, type="b")
if (NMDataset == "Theoph") xyplot(DV~TIME|ID, data=Theo, type="b", index.cond=list(order(as.numeric(levels(unique(Theo$ID))))))
dev.off()

if (Get_os() == "windows") {
} else {
    system('convert -density 300 result/xyplot.pdf result/xyplot.jpg')
    system("cp result/xyplot.jpg xyplot.jpg")
}
```

![Concentration-time curve of `r NMDataset`](xyplot.jpg)

### Method Calculation

- Dataset: `r NMDataset`
- Method: `r METHOD`

```{r ZERO}
PREDFILE <- ifelse(NMDataset == "Emax", "03-Emax/PRED.R", "04-THEO/PRED.R")

InitPara = InitStep(DataAll, THETAinit=THETAinit, OMinit=OMinit, SGinit=SGinit, 
                    nTheta=nTheta, LB=LB, UB=UB, METHOD=METHOD, PredFile=PREDFILE)

(EstRes = EstStep())           # 0.6200359 secs, 0.4930282 secs
(CovRes = CovStep())

PostHocEta() # FinalPara from EstStep()

get("EBE", envir=e)
```

## Appendix

### Examples for Initial Values

#### Emax
```
nTheta = 2
nEta = 1
nEps = 1

THETAinit = 10, 100
OMinit = 0.2
SGinit = 1
```

#### Theoph (ZERO, CONC)
```
nTheta = 3
nEta = 3
nEps = 2

THETAinit = 2, 50, 0.1
OMinit = 0.2, 0.1, 0.1, 0.1, 0.2, 0.1, 0.1, 0.1, 0.2
SGinit = 0.1, 0, 0, 0.1
```

#### Theoph (LAPL)

```
THETAinit = 4, 50, 0.2
```

The other values are the same with those of `Theoph (ZERO, CONC)`.

## Reference

`r paste(readLines("bibliography.txt"), collapse = "\n")`

## Bibliography