Documentation: FAQ

This documentation refers to version 4.0 for R. For previous versions for S-PLUS, click here.

 

Q.	How can I get help?
A.	All Xpose 4.0 functions are documented within the R help system. For example, if you want to know more about DV vs PRED plots and their options, type > ?dv.vs.pred at the R command line after loading Xpose. Also, a complete list of functions and their help entries may be found in the \chtml, \html and \latex directories of the five Xpose packages, found in the [R-HOME]\library folder. Formats are Microsoft compiled HTML, HTML, and LaTeX, respectively.
Q.	But what about human support?
A.	The frontline developer, Andrew Hooker [andrew.hooker(at)farmbio.uu.se] can assist.
Q.	Can I use Xpose 4.0 with S-PLUS?
A.	Unfortunately not. Xpose 4.0 was written for R, and while the dialect of S used in R is similar to the one found in S-PLUS, they are not 100% compatible.
Q.	Can I port Xpose 4.0 to S-PLUS, then?
A.	By all means. The source is freely available from SourceForge.net. We ask only that you share your modifications with the rest of us when they're done.
Q.	Does Xpose 4.0 work under Linux, UNIX or other non-Windows versions of R?
A.	Yes, since release 4.0 PR3-2 .
Q.	Can I create a version of Xpose for R on other operating systems?
A.	By all means. The source is freely available from SourceForge.net. We ask only that you share your modifications with the rest of us when they're done.
Q.	I've installed Xpose as the instructions direct, but when I try to load it using library(xpose4), it says: Loading required package: lattice Loading required package: grid Loading required package: Hmisc Error: package 'Hmisc' could not be loaded In addition: Warning message: there is no package called 'Hmisc' in: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc)
A.	You need the external library 'Hmisc' for Xpose 4.0PR2 onwards to work, and 'gam' for 4.0PR3 or better. You can (and should) install them thus: > install.packages("Hmisc") > install.packages("gam") from the R command line.
Q.	Xpose says it can't find any matching table files, but I have lots of them!
A.	There are two things to check here. Firstly, make sure R is looking in the right place. Use File -> Change dir... in Windows, or (for example) > setwd("c:/NMV/runs/") (Windows) > setwd("/home/me/nmv/runs/") (UNIX/Linux) to specify the folder in which your files may be found (it can be any folder, not necessarily the one in the example). Confirm it with > getwd() If that doesn't work, check your naming convention. Xpose looks for files according to the following pattern, where * is your run number: sdtab* Standard table file, containing ID, IDV, DV, PRED, IPRED, WRES, IWRES, RES, IRES, etc. patab* Parameter table, containing model parameters - THETAs, ETAs and EPSes catab* Categorical covariates, e.g. SEX, RACE cotab* Continuous covariates, e.g. WT, AGE extra*, mutab*, mytab*, xptab* Other variables you might need to have available to Xpose cwtab* Conditional weighted residual tables run*.mod Model specification file run*.lst NONMEM output Strictly, only sdtab* is needed for basic goodness-of-fit functionality, but patab*, cotab*, catab* and the NONMEM input and output are recommended to get the full benefit from Xpose. You can use code similar to the following to generate the tables you need. NONMEM automatically appends DV, PRED, WRES and RES unless NOAPPEND is specified. Don't forget to leave at least one blank line at the end of the model specification file. $TABLE ID TIME IPRED IWRES EVID MDV           NOPRINT ONEHEADER FILE=sdtab1 $TABLE ID CL V2 KA K SLP KENZ        NOPRINT ONEHEADER FILE=patab1 $TABLE ID WT HT AGE BMI PKG       NOPRINT ONEHEADER FILE=cotab1 $TABLE ID SEX SMOK ALC        NOPRINT ONEHEADER FILE=catab1
Q.	What are these CWRES things?
A.	In short, CWRES are conditional weighted residuals, a better alternative to WRES with the FOCE method in NONMEM. Read more about them here. Documentation about how to use them is covered in some detail in the online help, under compute.cwres: > library(xpose4) > ?compute.cwres
Q.	How can I save my Xpose plots to a file ?
A.	Rather than saving a graphics windows, consider piping the output to a file. R provides a number of what it calls 'devices' to facilitate this. The onscreen image you see when you run an Xpose function is one such device - either "windows" (for Windows) or "x11" (for Linux or UNIX). These are the defaults. If you, however, want to send the output to a file, have a look in the R help for 'Devices' (?Devices) and see if there's something there that you can use. An example, for PDF: > library(xpose4) > xpdb5 <- xpose.data(5) > pdf(file="Xpose.pdf", paper="A4") > basic.gof(xpdb5) > dev.off() This will create an A4-sized PDF file in your working directory containing basic goodness-of-fit plots for run 5. It is essential to use dev.off() to close the file before you try and look at it.

 

Installation

Last updated: 2006-04-25, by Justin Wilkins

Xpose is distributed in a binary form as well as source code. The easiest way to install Xpose is to use the binaries but it may be desirable to compile Xpose yourself. The latter is necessary if there is no binary version available for your operating system, or if you need to customize Xpose. The installation instructions differ slightly depending on your operating system.

Xpose 4

• Install from R, by using the GUI (Packages -> Install package(s) from local zip files...). Navigate to the location of the downloaded file, select it, and R will do the rest.
  
  OR
  
  
• Unpack the Xpose distribution (you can use 7-Zip to do this, for example). This will create the directories xpose4, xpose4classic, xpose4data, xpose4generic and xpose4specific.
  
  
• Copy the xpose4, xpose4classic, xpose4data, xpose4generic and xpose4specific directories to the library directory of your R installation. The location of this varies depending on your R version but is usually something like:
  
  c:\Program Files\R\R-2.3.0\library

Done!

Xpose 3

UNIX/Linux - binary installation

Replace Splus5 with the command you use to run S-PLUS (e.g. Splus6).

• Unpack the Xpose distribution:
  % gunzip xp3104.tar.gz
  % tar xf xp3104.tar
  
  This will create a directory xpose31.
  
  
• Move the xpose31 directory to /SHOME/library where SHOME is the top directory of the S-PLUS installation tree. You should now have: /SHOME/library/xpose31.

Done!

UNIX/Linux - installation from source code

• Follow the steps for a binary installation above.
  
  
• cd to the new directory:
  % cd /SHOME/library/xpose31
  
  
• Remove the .Data directory
  % rm -rf .Data
  
  
• Create a new CHAPTER
  % Splus5 CHAPTER
  
  
• Start S-PLUS and source the Xpose installation function:
  % Splus5
  > source("Src/install.xpose.S")
  
  
• Install Xpose
  > install.xpose()

Done!

MS Windows - binary installation

• Unpack the Xpose distribution (you can use 7-Zip to do this, for example). This will create the directory xpose31.
  
  
• Copy the xpose31 directory to the library directory of your S-PLUS installation. The location of this varies depending on your S-PLUS version but is usually something like:
  c:\Program Files\Sp2000\library
  or
  c:\Program Files\Insightful\Splus6\library.

Done!

MS Windows & S-Plus 2000 - installation from source code

• Follow the steps for a binary installation above.
  
  
• Remove the _Data directory in the xpose31 directory.
  
  
• Start S-PLUS 2000.
  
  
• Create a new Workspace in the xpose31 directory - File|Workspace|New. Browse to the xpose31 directory and click OK.
  
  
• Open a Commands Window and type: source("Src/install.xpose.S")
  
  
• Install Xpose
  > install.xpose()

Done!

MS Windows & S-Plus 6 - installation from source code

• Follow the steps for a binary installation above.
  
  
• Remove the .Data directory in the xpose31 directory.
  
  
• Start S-PLUS 6.
  
  
• Create a new CHAPTER in the xpose31 directory: File|Chapters|New Working Chapter. Browse to the xpose31 directory and click OK.
  
  
• Open a Commands Window and type: source("Src/install.xpose.S")
  
  
• Install Xpose
  > install.xpose()

Running Xpose

Xpose 3 (in S-PLUS):

> library(xpose31)
> xpose31()

Xpose 4 (in R):

> library(xpose4)
> xpose4()

 

Terms of usage

Starting with Xpose 3.102 the terms of usage has changed and is now released under the GNU Lesser General Public License. A summary of the usage conditions are provided below.

 

Xpose - an S/R-based population PK/PD model building aid for NONMEM.
Copyright (C) 1999-2005 Niclas Jonsson and Mats Karlsson

This library 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 2.1 of the license, or (at your option) any later version.

This library 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.

You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

Niclas Jonsson
Division of Pharmacokinetics & Drug Therapy
Department of Pharmaceutical Biosciences
Uppsala University
Niclas.Jonsson@farmbio.uu.se