# Diagnostics for Nonlinear Mixed-Effect Models

## Documentation for package ‘xpose4’ version 4.7.4

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E G I K L M N P R S T W X

xpose4-package | The Xpose Package

## -- A --

absval.cwres.vs.cov.bw | Absolute conditional weighted residuals vs covariates for Xpose 4
absval.cwres.vs.pred | Absolute population conditional weighted residuals vs population predictions for Xpose 4
absval.cwres.vs.pred.by.cov | Absolute value of the conditional weighted residuals vs. population predictions, conditioned on covariates, for Xpose 4
absval.dcwres.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4
absval.dipred.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4
absval.diwres.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4
absval.dpred.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4
absval.dwres.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, 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
absval.iwres.vs.cov.bw | box and whisker plots of the absolute value of the individual weighted residuals vs. covariates
absval.iwres.vs.idv | absolute value of the individual weighted residuals vs. the independent variable
absval.iwres.vs.ipred | Absolute individual weighted residuals vs individual predictions for Xpose 4
absval.iwres.vs.ipred.by.cov | Absolute individual weighted residuals vs individual predictions, conditioned on covariates, for Xpose 4
absval.iwres.vs.pred | Absolute individual weighted residuals vs population predictions or independent variable for Xpose 4
absval.iwres.wres.vs.ipred.pred | Absolute population weighted residuals vs population predictions, and absolute individual weighted residuals vs individual predictions, for Xpose 4
absval.wres.vs.cov.bw | Absolute weighted residuals vs covariates for Xpose 4
absval.wres.vs.idv | Absolute value of (C)WRES vs. independent variable plot in Xpose4.
absval.wres.vs.pred | Absolute population weighted residuals vs population predictions for Xpose 4
absval.wres.vs.pred.by.cov | Absolute population weighted residuals vs population predictions, conditioned on covariates, for Xpose 4
absval_delta_vs_cov_model_comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4
add.absval | Column-transformation functions for Xpose 4
add.dichot | Column-transformation functions for Xpose 4
add.exp | Column-transformation functions for Xpose 4
add.grid.table | Print tables or text in a grid object
add.grid.text | Print tables or text in a grid object
add.log | Column-transformation functions for Xpose 4
add.model.comp | Additional model comparison plots, for Xpose 4
add.tad | Column-transformation functions for Xpose 4
addit.gof | Additional goodness-of-fit plots, for Xpose 4
add_transformed_columns | Column-transformation functions for Xpose 4
autocorr.cwres | Autocorrelation of conditional weighted residuals for Xpose 4
autocorr.iwres | autocorrelation of the individual weighted residuals
autocorr.wres | Autocorrelation of weighted residuals for Xpose 4

## -- B --

basic.gof | Basic goodness-of-fit plots, for Xpose 4
basic.model.comp | Basic model comparison plots, for Xpose 4
boot.hist | Function to create histograms of results from the 'bootstrap' tool in PsN
bootgam.print | Print summary information for a bootgam or bootscm
bootscm.import | Import bootscm data into R/Xpose

## -- C --

calc.npar | Read NONMEM output files into Xpose 4
cat.dv.vs.idv.sb | Categorical observations vs. independent variable using stacked bars.
cat.pc | Categorical (visual) predictive check.
change.ab.graph.par | Functions changing variable definitions in Xpose 4
change.bw.graph.par | Functions changing variable definitions in Xpose 4
change.cat.cont | Functions changing miscellaneous parameter settings in Xpose 4
change.cat.cont<- | Functions changing miscellaneous parameter settings in Xpose 4
change.cat.levels | Functions changing miscellaneous parameter settings in Xpose 4
change.cat.levels<- | Functions changing miscellaneous parameter settings in Xpose 4
change.cond.graph.par | Functions changing variable definitions in Xpose 4
change.dil.graph.par | Functions changing variable definitions in Xpose 4
change.dv.cat.levels | Functions changing miscellaneous parameter settings in Xpose 4
change.dv.cat.levels<- | Functions changing miscellaneous parameter settings in Xpose 4
change.label.par | Functions changing variable definitions in Xpose 4
change.lm.graph.par | Functions changing variable definitions in Xpose 4
change.misc.graph.par | Functions changing variable definitions in Xpose 4
change.miss | Functions changing miscellaneous parameter settings in Xpose 4
change.parm | Change parameter scope.
change.pi.graph.par | Functions changing variable definitions in Xpose 4
change.smooth.graph.par | Functions changing variable definitions in Xpose 4
change.subset | Functions changing miscellaneous parameter settings in Xpose 4
change.var.name | Changes the name of an Xpose data item
change.xlabel | Changes the label of an Xpose data item
change.xvardef | Change Xpose variable definitions.
change.xvardef<- | Change Xpose variable definitions.
change_graphical_parameters | Functions changing variable definitions in Xpose 4
change_misc_parameters | Functions changing miscellaneous parameter settings in Xpose 4
character_or_NULL-class | Class for creating multiple plots in xpose
character_or_numeric-class | Class "xpose.prefs"
compute.cwres | Compute the Conditional Weighted Residuals
cov.hist | Plot the parameter or covariate distributions using a histogram
cov.qq | Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots
cov.splom | Plot scatterplot matrices of parameters, random parameters or covariates
cov.summary | Summarize individual parameter values and covariates
create.parameter.list | Read NONMEM output files into Xpose 4
create.xpose.plot.classes | Create xpose.multiple.plot class.
createXposeClasses | This function creates the Xpose data classes ("xpose.data" and "xpose.prefs")
cwres.dist.hist | Histogram of conditional weighted residuals (CWRES), for Xpose 4
cwres.dist.qq | Quantile-quantile plot of conditional weighted residuals (CWRES), for Xpose 4
cwres.vs.cov | Conditional Weighted residuals (CWRES) plotted against covariates, for Xpose 4
cwres.vs.idv | Population conditional weighted residuals (CWRES) plotted against the independent variable (IDV) for Xpose 4
cwres.vs.idv.bw | Box-and-whisker plot of conditional weighted residuals vs the independent variable for Xpose 4
cwres.vs.pred | Population conditional weighted residuals (CWRES) plotted against population predictions (PRED) for Xpose 4
cwres.vs.pred.bw | Box-and-whisker plot of conditional weighted residuals vs population predictions for Xpose 4
cwres.wres.vs.idv | Weighted residuals (WRES) and conditional WRES (CWRES) plotted against the independent variable (IDV)
cwres.wres.vs.pred | Weighted residuals (WRES) and conditional WRES (CWRES) plotted against the population predictions (PRED)

## -- D --

Data | Extract or assign data from an xpose.data object.
data.checkout | Check through the source dataset to detect problems
data.frame_or_NULL-class | Class xpose.data
Data<- | Extract or assign data from an xpose.data object.
data_extract_or_assign | Extract or assign data from an xpose.data object.
db.names | Prints the contents of an Xpose data object
dOFV.vs.cov | Change in individual objective function value vs. covariate value.
dOFV.vs.id | Change in Objective function value vs. removal of individuals.
dOFV1.vs.dOFV2 | Change in individual objective function value 1 vs. individual objective function value 2.
dv.preds.vs.idv | Observations (DV), individual predictions (IPRED) and population predictions (IPRED) plotted against the independent variable (IDV), for Xpose 4
dv.vs.idv | Observations (DV) plotted against the independent variable (IDV) for Xpose 4
dv.vs.ipred | Observations (DV) plotted against individual predictions (IPRED) for Xpose 4
dv.vs.ipred.by.cov | Dependent variable vs individual predictions, conditioned on covariates, for Xpose 4
dv.vs.ipred.by.idv | Dependent variable vs individual predictions, conditioned on independent variable, for Xpose 4
dv.vs.pred | Observations (DV) plotted against population predictions (PRED) for Xpose 4
dv.vs.pred.by.cov | Dependent variable vs population predictions, conditioned on covariates, for Xpose 4
dv.vs.pred.by.idv | Dependent variable vs population predictions, conditioned on independent variable, for Xpose 4
dv.vs.pred.ipred | Observations (DV) are plotted against individual predictions (IPRED) and population predictions (PRED), for Xpose 4

## -- E --

export.graph.par | Exports Xpose graphics settings to a file.
export.variable.definitions | Exports Xpose variable definitions to a file from an Xpose data object.

## -- G --

GAM_summary_and_plot | GAM functions for Xpose 4
get.doc | Functions changing miscellaneous parameter settings in Xpose 4
gof | Structured goodness of fit diagnostics.
gofSetup | Structured goodness of fit diagnostics.

## -- I --

import.graph.par | Imports Xpose graphics settings from a file to an Xpose data object.
import.variable.definitions | Imports Xpose variable definitions from a file to an Xpose data object.
ind.cwres | Compute the Conditional Weighted Residuals
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
ind.plots.cwres.hist | Histograms of weighted residuals for each individual in an Xpose data object, for Xpose 4
ind.plots.cwres.qq | Quantile-quantile plots of weighted residuals for each individual in an Xpose data object, for Xpose 4
ind.plots.wres.hist | Histograms of weighted residuals for each individual in an Xpose data object, for Xpose 4
ind.plots.wres.qq | Quantile-quantile plots of weighted residuals for each individual in an Xpose data object, for Xpose 4
ipred.vs.idv | Individual predictions (IPRED) plotted against the independent variable (IDV) for Xpose 4
is.cwres.readable.file | Compute the Conditional Weighted Residuals
iwres.dist.hist | Histogram of individual weighted residuals (IWRES), for Xpose 4
iwres.dist.qq | Quantile-quantile plot of individual weighted residuals (IWRES), for Xpose 4
iwres.vs.idv | Individual weighted residuals (IWRES) plotted against the independent variable (IDV) for Xpose 4

## -- K --

kaplan.plot | Kaplan-Meier plots of (repeated) time-to-event data

## -- L --

list_or_NULL-class | Class for creating multiple plots in xpose
logical_or_numeric-class | Class for creating multiple plots in xpose

## -- M --

make.sb.data | Make stacked bar data set.

## -- N --

npc.coverage | Function to plot the coverage of the Numerical Predictive Check
nsim | Extract or set the value of the Nsim slot.
nsim<- | Extract or set the value of the Nsim slot.
numeric_or_NULL-class | Class xpose.data

## -- P --

parm.hist | Plot the parameter or covariate distributions using a histogram
parm.qq | Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots
parm.splom | Plot scatterplot matrices of parameters, random parameters or covariates
parm.summary | Summarize individual parameter values and covariates
parm.vs.cov | Parameters plotted against covariates, for Xpose 4
parm.vs.parm | Plot parameters vs other parameters
par_cov_hist | Plot the parameter or covariate distributions using a histogram
par_cov_qq | Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots
par_cov_splom | Plot scatterplot matrices of parameters, random parameters or covariates
par_cov_summary | Summarize individual parameter values and covariates
pred.vs.idv | Population predictions (PRED) plotted against the independent variable (IDV) for Xpose 4
print-method | Create xpose.multiple.plot class.
print.xpose.multiple.plot | Print an Xpose multiple plot object.

## -- R --

randtest.hist | Function to create a histogram of results from the randomization test tool ('randtest') in PsN
ranpar.hist | Plot the parameter or covariate distributions using a histogram
ranpar.qq | Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots
ranpar.splom | Plot scatterplot matrices of parameters, random parameters or covariates
ranpar.vs.cov | Random parameters plotted against covariates, for Xpose 4
read.cwres.data | Compute the Conditional Weighted Residuals
read.lst | Read NONMEM output files into Xpose 4
read.nm.tables | Reading NONMEM table files
read.npc.vpc.results | Read the results file from a Numerical or Visual Predictive Check run in PsN
read.TTE.sim.data | Read (repeated) time-to-event simulation data files.
read.vpctab | Read the vpctab file from PsN into Xpose
read_NM_output | Read NONMEM output files into Xpose 4
read_nm_table | Read NONMEM table files produced from simulation.
reset.graph.par | Resets Xpose variable definitions to factory settings
runsum | Print run summary in Xpose 4

## -- S --

SData | Extract or assign data from an xpose.data object.
SData<- | Extract or assign data from an xpose.data object.
set.doc | Functions changing miscellaneous parameter settings in Xpose 4
simpraz.xpdb | Simulated prazosin Xpose database.
simprazExample | Function to create files for the simulated prazosin example in Xpose
sqrtm | Compute the Conditional Weighted Residuals

## -- T --

tabulate.parameters | Tabulate the population parameter estimates

## -- W --

wres.dist.hist | Histogram of weighted residuals (WRES), for Xpose 4
wres.dist.qq | Quantile-quantile plot of weighted residuals (WRES), for Xpose 4
wres.vs.cov | Weighted residuals (WRES) plotted against covariates, for Xpose 4
wres.vs.idv | Population weighted residuals (WRES) plotted against the independent variable (IDV) for Xpose 4
wres.vs.idv.bw | Box-and-whisker plot of weighted residuals vs the independent variable for Xpose 4
wres.vs.pred | Population weighted residuals (WRES) plotted against population predictions (PRED) for Xpose 4
wres.vs.pred.bw | Box-and-whisker plot of weighted residuals vs population predictions for Xpose 4

## -- X --

xlabel | Extract and set labels for Xpose data items.
xlabel<- | Extract and set labels for Xpose data items.
xp.akaike.plot | GAM functions for Xpose 4
xp.boot.par.est | Compare parameter estimates for covariate coefficients
xp.boot.par.est.corr | Correlations between covariate coefficients
xp.cook | GAM functions for Xpose 4
xp.daic.npar.plot | Distribution of difference in AIC
xp.distr.mod.size | Plot of model size distribution for a bootgam or bootscm
xp.dofv.npar.plot | Distribution of difference in OFV
xp.dofv.plot | OFV difference (optimism) plot.
xp.get.disp | Default function for calculating dispersion in 'xpose.gam'.
xp.inc.cond.stab.cov | Trace plots for conditional indices
xp.inc.ind.cond.stab.cov | Trace plots for conditional indices rper replicate number
xp.inc.prob | Inclusion frequency plot
xp.inc.prob.comb.2 | Inclusion frequency plot for combination of covariates.
xp.inc.stab.cov | Inclusion stability plot A plot of the inclusion frequency of covariates vs bootgam/bootscm iteration number. This plot can be used to evaluate whether sufficient iterations have been performed.
xp.incl.index.cov | Plot of inclusion index of covariates.
xp.incl.index.cov.comp | Inclusion index individuals, compare between covariates.
xp.incl.index.cov.ind | Individual inclusion index
xp.ind.inf.fit | GAM functions for Xpose 4
xp.ind.inf.terms | GAM functions for Xpose 4
xp.ind.stud.res | GAM functions for Xpose 4
xp.plot | GAM functions for Xpose 4
xp.scope3 | Define a scope for the gam. Used as default input to the 'scope' argument in 'xpose.gam'
xp.summary | GAM functions for Xpose 4
xpose | The Xpose Package
xpose.bootgam | Title
xpose.calculate.cwres | Compute the Conditional Weighted Residuals
xpose.data | Create an Xpose data object
xpose.data-class | Class xpose.data
xpose.gam | Stepwise GAM search for covariates on a parameter (Xpose 4)
xpose.license.citation | Displays the Xpose license and citation information
xpose.logTicks | Functions to create nice looking axes when using Log scales.
xpose.multiple.plot | Create and object with class "xpose.multiple.plot".
xpose.multiple.plot-class | Class for creating multiple plots in xpose
xpose.multiple.plot.default | Xpose 4 generic function for plotting multiple lattice objects on one page
xpose.panel.bw | Default box-and-whisker panel function for Xpose 4
xpose.panel.default | Default panel function for Xpose 4
xpose.panel.histogram | Default histogram panel function for Xpose 4
xpose.panel.qq | Default QQ panel function for Xpose 4
xpose.panel.splom | Scatterplot matrix panel function for Xpose 4
xpose.plot.bw | The generic Xpose functions for box-and-whisker plots
xpose.plot.default | The Xpose 4 generic functions for continuous y-variables.
xpose.plot.histogram | The Xpose 4 generic functions for continuous y-variables.
xpose.plot.qq | The generic Xpose functions for QQ plots
xpose.plot.splom | The Xpose 4 generic functions for scatterplot matrices.
xpose.prefs-class | Class "xpose.prefs"
xpose.print | Summarize an xpose database
xpose.read | Imports Xpose graphics settings from a file to an Xpose data object.
xpose.string.print | Print a pretty string.
xpose.VPC | Visual Predictive Check (VPC) using XPOSE
xpose.VPC.both | Xpose Visual Predictive Check (VPC) for both continuous and Limit of Quantification data.
xpose.VPC.categorical | Xpose visual predictive check for categorical data.
xpose.write | Exports Xpose graphics settings to a file.
xpose.xscale.components.log10 | Functions to create nice looking axes when using Log scales.
xpose.yscale.components.log10 | Functions to create nice looking axes when using Log scales.
xpose4 | Classic menu system for Xpose 4
xpPage | Structured goodness of fit diagnostics.
xsubset | Extract or set the value of the Subset slot.
xsubset<- | Extract or set the value of the Subset slot.
xvardef | Extract and set Xpose variable definitions.
xvardef<- | Extract and set Xpose variable definitions.