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' )
by Andrew C. Hooker, Mats O. Karlsson and E. Niclas Jonsson
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.
To install xpose you will need R (>= version 2.2.0).
To install Xpose in R use one of the following methods:
latest stable release -- From CRAN. Write at the R command line:
r
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
devtools::install_github("UUPharmacometrics/xpose4") ```
Start R and load xpose:
library(xpose4)
To use the classic menu system, type at the R command prompt:
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
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
xpdb <- xpose.data(1)
xpdb <- simpraz.xpdb
Display goodness-of-fit plots:
basic.gof(xpdb)
Clean up files that were created to show these examples:
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.
A more detailed description of Xpose with example plots and explanaitions for most of the functions in the package is available in our Bestiarium: https://xpose.sourceforge.net/bestiarium_v1.0.pdf
Andrew Hooker (andrew.hooker at farmaci.uu.se) should be able to get you an answer if you run into trouble. The website https://uupharmacometrics.github.io/xpose4/ should also be of help.
Bugfix releases will be released regularly, fixing any problems that are found.
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 https://www.gnu.org/licenses/.
None at present, but there will certainly be a few. Report them at https://github.com/UUPharmacometrics/xpose4/issues.
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