README.Rmd

---
output:
  github_document:
    html_preview: false
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = 'man/figures/'#,
  #fig.dpi    = 96,
  #fig.height = 4, 
  #fig.width  = 4, 
  #out.width  = '50%', 
  #fig.align  = 'center'
)
```

# Xpose 4 <a href="https://uupharmacometrics.github.io/xpose4/"><img src="man/figures/xposelogo.png" align="right" /></a>

[![Travis-CI Build Status](https://travis-ci.org/UUPharmacometrics/xpose4.svg?branch=master)](https://travis-ci.org/UUPharmacometrics/xpose4)
[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/xpose4)](https://CRAN.R-project.org/package=xpose4) 
[![codecov.io](https://codecov.io/github/UUPharmacometrics/xpose4/coverage.svg?branch=master)](https://codecov.io/github/UUPharmacometrics/xpose4?branch=master)


by Andrew C. Hooker, Mats O. Karlsson and E. Niclas Jonsson

http://xpose.sourceforge.net/


## Introduction

Xpose 4 is a collection of functions to be used as a model
building aid for nonlinear mixed-effects (population) analysis
using NONMEM. It facilitates data set checkout, exploration and
visualization, model diagnostics, candidate covariate identification
and model comparison.

## Installation

To install xpose you will need R (>= version 2.2.0). Download the latest version of R from http://www.r-project.org.  
To install Xpose in R use one of the following methods:

* latest stable release -- From CRAN.  Write at the R command line:

    ```{r standard-installation, eval = FALSE}
    install.packages("xpose4")
    ```
     
* Latest development version -- from Github. Note that the command below installs the "master" 
(development) branch; if you want the release branch from Github add `ref="release"` to the
`install_github()` call. 

    ```{r gh-installation, eval = FALSE}
    # install.packages("devtools")
    devtools::install_github("UUPharmacometrics/xpose4")
    ```

## Running Xpose 4

Start R and load xpose:
```{r}
library(xpose4)
```


To use the classic menu system, type at the R command prompt:
```{r classic-menu,eval=FALSE}
xpose4()
```

Each function is independently available from the command
line, once the Xpose library is loaded. 

First we create a set of files from a NONMEM run
```{r,eval=FALSE}
cur.files <- dir() # current files in temp directory

simprazExample() # write files from an example NONMEM run
new.files <- dir()[!(dir() %in% cur.files)]  # the new files created by simprazExample
```

Then we can import our files to Xpose

```{r,eval=FALSE}
xpdb <- xpose.data(1) 
```


```{r,echo=FALSE}
xpdb <- simpraz.xpdb
```


Display goodness-of-fit plots:

```{r readme_example_figure_1}
  basic.gof(xpdb)
```

Clean up files that were created to show these examples:
```{r,eval=FALSE}
unlink(new.files)
```


More help is available in the online documentation, which can be found by
typing (for example) `?xpose4` at the R command line.  


## The Xpose 4 Bestiary

A more detailed description of Xpose with example plots and explanaitions for
most of the functions in the package is available in our Bestiarium: 
http://xpose.sourceforge.net/bestiarium_v1.0.pdf


## Don't Panic

Andrew Hooker (andrew.hooker at farmbio.uu.se)
should be able to get you an answer if you run into trouble.  The
website http://xpose.sf.net  should also be of help.


## Release Schedule

Bugfix releases will be released regularly, fixing any problems that are
found. 


## License

Xpose 4 is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Lesser General Public License for more details 
<http://www.gnu.org/licenses/>.


## Known Bugs

None at present, but there will certainly be a few