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:
Latest development version – from Github. Note that the command below installs the “master” (development) branch; if you want the release branch from Github add
# install.packages("devtools") devtools::install_github("UUPharmacometrics/xpose4")
Running Xpose 4
Start R and load xpose:
To use the classic menu system, type at the R command prompt:
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)
Display goodness-of-fit plots:
Clean up files that were created to show these examples:
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
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.
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.