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Xpose 4

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

http://xpose.sourceforge.net/

Introduction

Xpose 4 is a ground-floor rewrite of Xpose 3.1. Chief amongst the enhancements in the new version is the migration from S-PLUS to R, a free, multi-platform statistical environment. We have also added direct access to Xpose functions from the command line, and, through R, access to Xpose tools by third-party applications.

R and required package installation

To install xpose you will need:

  • R version >=2.2.0. Download the latest version of R from www.r-project.org.
  • the gam package. Install the latest version from CRAN. Write at the R command

line (type ?install.packages in R for more details):

install.packages("gam")

Xpose 4 Installation

Install xpose in R using one of the following methods:

  • latest stable release -- From CRAN. Write at the R command line:
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. The install_github() approach requires that you build from source, i.e. make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.

devtools::install_github("xpose4",username="andrewhooker")

Additional recommended packages

The Hmisc package is also recommended. to install, write at the R command line (type ?install.packages in R for more details):

install.packages("Hmisc")

Running Xpose 4

Start R

To use the classic menu system, type at the R command prompt:

library(xpose4)
xpose4()

Each function is independently available from the command line, once the Xpose library is loaded. For example, assuming your run is called 'run5.mod', you might do the following:

  • Import data
  xpdb5 <- xpose.data(5)
  • Display goodness-of-fit plots
  basic.gof(xpdb5)

More help is available in the online documentation, which can be found by typing (for example) ?xpose 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

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Version

Install

install.packages('xpose4')

Monthly Downloads

507

Version

4.5.3

License

LGPL (>= 3)

Maintainer

Andrew C Hooker

Last Published

November 24th, 2014

Functions in xpose4 (4.5.3)

absval.delta.model.comp

Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4
ind.plots

Observations (DV), individual predictions (IPRED) and population predictions (PRED) are plotted against the independent variable for every individual in the dataset, for Xpose 4
dv.vs.pred.by.cov

Dependent variable vs population predictions, conditioned on covariates, for Xpose 4
cwres.vs.idv

Population conditional weighted residuals (CWRES) plotted against the independent variable (IDV) for Xpose 4
absval.iwres.vs.ipred.by.cov

Absolute individual weighted residuals vs individual predictions, conditioned on covariates, for Xpose 4
change.misc.parameters

Functions changing miscellaneous parameter settings in Xpose 4
dv.vs.pred.by.idv

Dependent variable vs population predictions, conditioned on independent variable, for Xpose 4
create.xpose.plot.classes

Create xpose.multiple.plot class.
simprazExample

Function to create files for the simulated Prazosin example in Xpose
boot.hist

Function to create histograms of results from the bootstrap tool in PsN
cwres.vs.idv.bw

Box-and-whisker plot of conditional weighted residuals vs the independent variable for Xpose 4
dv.vs.ipred

Observations (DV) plotted against individual predictions (IPRED) for Xpose 4
read.TTE.sim.data

Read (repeated) time-to-event simulation data files.
bootgam.print

Print summary information for a bootgam or bootscm
absval.wres.vs.cov.bw

Absolute weighted residuals vs covariates for Xpose 4
cat.dv.vs.idv.sb

Categorical observations vs. idependent variable using stacked bars.
cwres.vs.pred.bw

Box-and-whisker plot of conditional weighted residuals vs population predictions for Xpose 4
functions

Data functions for Xpose 4
iwres.vs.idv

Individual weighted residuals (IWRES) plotted against the independent variable (IDV) for Xpose 4
wres.dist.qq

Quantile-quantile plot of weighted residuals (WRES), for Xpose 4
pred.vs.idv

Population predictions (PRED) plotted against the independent variable (IDV) for Xpose 4
compute.cwres

Compute the Conditional Weighted Residuals
gof

Structured goodness of fit diagnostics.
change.xlabel

Changes the label of an Xpose data item
absval.wres.vs.idv

Absolute value of (C)WRES vs. independent variable plot in Xpose4.
absval.iwres.vs.ipred

Absolute individual weighted residuals vs individual predictions for Xpose 4
add.functions

Column-transformation functions for Xpose 4
wres.dist.hist

Histogram of weighted residuals (WRES), for Xpose 4
ipred.vs.idv

Individual predictions (IPRED) plotted against the independent variable (IDV) for Xpose 4
ind.plots.wres.hist

Histograms of weighted residuals for each individual in an Xpose data object, for Xpose 4
change.var.name

Changes the name of an Xpose data item
dv.vs.pred.ipred

Observations (DV) are plotted against individual predictions (IPRED) and population predictions (PRED), for Xpose 4
addit.gof

Additional goodness-of-fit plots, for Xpose 4
autocorr.cwres

Autocorrelation of conditional weighted residuals for Xpose 4
absval.cwres.vs.pred

Absolute population conditional weighted residuals vs population predictions for Xpose 4
read.npc.vpc.results

Read the results file from a Numerical or Visual Predictive Check run in PsN
cwres.dist.qq

Quantile-quantile plot of conditional weighted residuals (CWRES), for Xpose 4
wres.vs.idv.bw

Box-and-whisker plot of weighted residuals vs the independent variable for Xpose 4
absval.iwres.cwres.vs.ipred.pred

Absolute population weighted residuals vs population predictions, and absolute individual weighted residuals vs individual predictions, for Xpose 4
data.checkout

Check through the source dataset to detect problems
read.nm.tables

Reading NONMEM table files
Data

Extract data from an xpose.data object.
classic

Classic menu functions for Xpose 4
ind.plots.wres.qq

Quantile-quantile plots of weighted residuals for each individual in an Xpose data object, for Xpose 4
createXposeClasses

This function creates the Xpose data classes ("xpose.data" and "xpose.prefs")
wres.vs.pred

Population weighted residuals (WRES) plotted against population predictions (PRED) for Xpose 4
cwres.vs.cov

Conditional Weighted residuals (CWRES) plotted against covariates, for Xpose 4
autocorr.wres

Autocorrelation of weighted residuals for Xpose 4
basic.model.comp

Basic model comparison plots, for Xpose 4
wres.vs.pred.bw

Box-and-whisker plot of weighted residuals vs population predictions for Xpose 4
absval.wres.vs.pred

Absolute population weighted residuals vs population predictions for Xpose 4
dOFV1.vs.dOFV2

Change in individual objective function value 1 vs. individual objective function value 2.
parm.splom

Plot scatterplot matrices of parameters, random parameters or covariates
absval.cwres.vs.cov.bw

Absolute conditional weighted residuals vs covariates for Xpose 4
generic

Generic internal functions for Xpose 4
cat.pc

Categorical (visual) predictive check.
change.graphical.parameters

Functions changing variable definitions in Xpose 4
export.graph.par

Exports Xpose graphics settings to a file.
ranpar.vs.cov

Random parameters plotted against covariates, for Xpose 4
xpose.VPC.categorical

Xpose visual predictive check for categorical data.
absval.cwres.vs.pred.by.cov

Absolute value of the conditional weighted residuals vs. population predictions, conditioned on covariates, for Xpose 4
parm.vs.cov

Parameters plotted against covariates, for Xpose 4
internal.functions

Internal functions for the VPC
add.model.comp

Additional model comparison plots, for Xpose 4
parm.vs.parm

Plot parameters vs other parameters
dist.hist

Plot the parameter or covariate distributions using a histogram
make.sb.data

Make stacked bar data set.
xpose.plot.bw

The generic Xpose functions for box-and-whisker plots
create.mirror

Function to create mirror plots from the generic Xpose plotting commands
runsum

Print run summary in Xpose 4
cwres.dist.hist

Histogram of conditional weighted residuals (CWRES), for Xpose 4
dOFV.vs.id

Change in Objective function value vs. removal of individuals.
xpose.data-class

Class xpose.data
gam.functions

GAM functions for Xpose 4
change.xvardef

Change Xpose variable definitions.
xpose.create.title.text

Create Xpose title text for plots.
dv.vs.ipred.by.idv

Dependent variable vs individual predictions, conditioned on independent variable, for Xpose 4
wres.vs.idv

Population weighted residuals (WRES) plotted against the independent variable (IDV) for Xpose 4
xpose.prefs-class

Class "xpose.prefs"
dist.qq

Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots
reset

Resets Xpose variable definitions to factory settings
tabulate.parameters

Tabulate the population parameter estimates
simpraz.xpdb

Simulated prazosin Xpose database.
xpose.multiple.plot

Create and object with class "xpose.multiple.plot".
tables

Generic table functions for Xpose 4
xpose.yscale.components.log10

Functions to create nice looking axes when using Log scales.
xpose.ask.for.filename

Function to ask the user for the name of a file
xpose.VPC

Visual Predictive Check (VPC) using XPOSE
xp.inc.prob

Inclusion frequency plot
xp.inc.prob.comb.2

Inclusion frequency plot for combination of covariates.
xp.boot.par.est.corr

Correlations between covariate coefficients
bootscm.import

Import bootscm data into R/Xpose
xp.inc.stab.cov

Inclusion stability plot
absval.wres.vs.pred.by.cov

Absolute population weighted residuals vs population predictions, conditioned on covariates, for Xpose 4
db.names

Prints the contents of an Xpose data object
dOFV.vs.cov

Change in individual objective function value vs. covariate value.
xpose.panel.bw

Default box-and-whisker panel function for Xpose 4
xpose.plot.splom

The Xpose 4 generic functions for scatterplot matrices.
npc.coverage

Function to plot the coverage of the Numerical Predictive Check
xpose4specific-internal

Internal xpose4specific Functions
xpose.dev.new

Create a new graphical device for an Xpose plot.
import.variable.definitions

Imports Xpose variable definitions from a file to an Xpose data object.
xpose4psn-package

Xpose PsN post-processing functions
xp.dofv.plot

OFV difference (optimism) plot.
xpose.panel.splom

Scatterplot matrix panel function for Xpose 4
iwres.dist.qq

Quantile-quantile plot of individual weighted residuals (IWRES), for Xpose 4
xp.incl.index.cov

Plot of inclusion index of covariates.
xpose.plot.default

The Xpose 4 generic functions for continuous y-variables.
xp.incl.index.cov.ind

Individual inclusion index
xvardef

Extracts and set Xpose variable definitions.
xpose.data

Creates an Xpose data object
dv.vs.pred

Observations (DV) plotted against population predictions (PRED) for Xpose 4
nsim

Extract or set the value of the Nsim slot.
summary

Summarize individual parameter values and covariates
xpose4generic-package

Xpose generic multi-purpose functions
export.variable.definitions

Exports Xpose variable definitions to a file from an Xpose data object.
Read NONMEM output files

Read NONMEM output files into Xpose 4
xpose.multiple.plot.default

Xpose 4 generic function for plotting multiple lattice objects on one page
xpose.panel.qq

Default QQ panel function for Xpose 4
print.xpose.multiple.plot

Print an Xpose multiple plot object.
xpose.plot.qq

The generic Xpose functions for QQ plots
read.vpctab

Read the vpctab file from PsN into Xpose
kaplan.plot

Kaplan-Meier plots of (repeated) time-to-event data
xpose4classic-internal

Internal xpose4classic Functions
wres.vs.cov

Weighted residuals (WRES) plotted against covariates, for Xpose 4
xpose.VPC.both

Xpose Visual Predictive Check (VPC) for both continuous and Limit of Quantification data.
dv.vs.ipred.by.cov

Dependent variable vs individual predictions, conditioned on covariates, for Xpose 4
xpose4classic-package

Xpose classic menu system
xpose4data-internal

Internal xpose4data Functions
xpose.string.print

Print a pretty string.
xpose4specific-package

Xpose specific functions for a single purpose
xpose.plot.histogram

The Xpose 4 generic functions for continuous y-variables.
xpose.create.title

Functions to create labels for plots
xpose.gam

Stepwise GAM search for covariates on a parameter (Xpose 4)
xpose4-package

The Xpose Package
xpose.panel.histogram

Default histogram panel function for Xpose 4
xpose.license.citation

Displays the Xpose license and citation information
xpose.panel.default

Default panel function for Xpose 4
xpose4data-package

Xpose database creation and manipulation
absval.iwres.vs.pred

Absolute individual weighted residuals vs population predictions or independent variable for Xpose 4
basic.gof

Basic goodness-of-fit plots, for Xpose 4
change.parm

Change parameter scope.
iwres.dist.hist

Histogram of individual weighted residuals (IWRES), for Xpose 4
randtest.hist

Function to create a histogram of results from the randomization test tool (randtest) in PsN
xp.distr.mod.size

Plot of model size distribution for a bootgam or bootscm
xlabel

Extract and set labels for Xpose data items.
xsubset

Extract or set the value of the Subset slot.
add.grid.table

Print tables or text in a grid object
cwres.wres.vs.idv

Weighted residuals (WRES) and conditional WRES (CWRES) plotted against the independent variable (IDV) or the population predictions (PRED) for Xpose 4
cwres.vs.pred

Population conditional weighted residuals (CWRES) plotted against population predictions (PRED) for Xpose 4
dv.vs.idv

Observations (DV) plotted against the independent variable (IDV) for Xpose 4
import.graph.par

Imports Xpose graphics settings from a file to an Xpose data object.
xp.boot.par.est

Compare parameter estimates for covariate coefficients
xp.incl.index.cov.comp

Inclusion index individuals, compare between covariates.