Diagnostics for Nonlinear Mixed-Effect Models

Documentation for package ‘xpose4’ version 4.7.3

Help Pages

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.