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xpose4 (version 4.5.0)

Xpose 4

Description

Xpose is collection of functions to be used as a model building aid for non-linear mixed effects (population) analysis using NONMEM. It facilitates data set checkout, exploration and visualization, model diagnostics, candidate covariate identification and model comparison.

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Install

install.packages('xpose4')

Monthly Downloads

478

Version

4.5.0

License

LGPL (>= 3)

Maintainer

Andrew C Hooker

Last Published

May 20th, 2014

Functions in xpose4 (4.5.0)

Change Xpose variable definitions.

Autocorrelation of conditional weighted residuals for Xpose 4

absval.cwres.vs.cov.bw

Absolute conditional weighted residuals vs covariates for Xpose 4

Categorical (visual) predictive check.

basic.model.comp

Basic model comparison plots, for Xpose 4

Changes the label of an Xpose data item

create.xpose.plot.classes

Create xpose.multiple.plot class.

Function to create histograms of results from the bootstrap tool in http://psn.sf.net{PsN}

Conditional Weighted residuals (CWRES) plotted against covariates, 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

Import bootscm data into R/Xpose

GAM functions for Xpose 4

dv.vs.ipred.by.idv

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

absval.iwres.vs.pred

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

Extract and set labels for Xpose data items.

absval.wres.vs.idv

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

cwres.vs.idv.bw

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

cwres.dist.hist

Histogram of conditional weighted residuals (CWRES), for Xpose 4

xp.inc.stab.cov

Inclusion stability plot

Basic goodness-of-fit plots, for Xpose 4

Print summary information for a bootgam or bootscm

Compute the Conditional Weighted Residuals

Random parameters plotted against covariates, for Xpose 4

absval.delta.model.comp

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

absval.iwres.vs.ipred

Absolute individual weighted residuals vs individual predictions for Xpose 4

Prints the contents of an Xpose data object

Data functions for Xpose 4

absval.wres.vs.pred

Absolute population weighted residuals vs population predictions for Xpose 4

Population conditional weighted residuals (CWRES) plotted against the independent variable (IDV) 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

Plot parameters vs other parameters

cat.dv.vs.idv.sb

Categorical observations vs. idependent variable using stacked bars.

Read the vpctab file from PsN into Xpose

Autocorrelation of weighted residuals for Xpose 4

Reading NONMEM table files

Generic internal functions for Xpose 4

change.graphical.parameters

Functions changing variable definitions in Xpose 4

createXposeClasses

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

xpose.yscale.components.log10

Functions to create nice looking axes when using Log scales.

Function to create mirror plots from the generic Xpose plotting commands

xp.distr.mod.size

Plot of model size distribution for a bootgam or bootscm

Change parameter scope.

tabulate.parameters

Tabulate the population parameter estimates

Parameters plotted against covariates, for Xpose 4

Default QQ panel function for Xpose 4

Change in individual objective function value vs. covariate value.

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

Population conditional weighted residuals (CWRES) plotted against population predictions (PRED) for Xpose 4

change.misc.parameters

Functions changing miscellaneous parameter settings in Xpose 4

Plot the parameter or covariate distributions using a histogram

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

Change in Objective function value vs. removal of individuals.

dv.vs.pred.ipred

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

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

Additional goodness-of-fit plots, for Xpose 4

Print tables or text in a grid object

change.var.name

Changes the name of an Xpose data item

xpose.data-class

Class xpose.data

xpose.create.title

Functions to create labels for plots

Quantile-quantile plot of individual weighted residuals (IWRES), for Xpose 4

Creates an Xpose data object

Individual weighted residuals (IWRES) plotted against the independent variable (IDV) for Xpose 4

Extract or set the value of the Subset slot.

Make stacked bar data set.

Observations (DV) plotted against the independent variable (IDV) for Xpose 4

xp.boot.par.est

Compare parameter estimates for covariate coefficients

Read NONMEM output files

Read NONMEM output files into Xpose 4

import.variable.definitions

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

dv.vs.ipred.by.cov

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

Xpose Visual Predictive Check (VPC) for both continuous and Limit of Quantification data.

Check through the source dataset to detect problems

export.variable.definitions

Exports Xpose variable definitions to a file from an Xpose data object.

Simulated prazosin Xpose database.

xpose.VPC.categorical

Xpose visual predictive check for categorical data.

cwres.vs.pred.bw

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

xp.boot.par.est.corr

Correlations between covariate coefficients

Additional model comparison plots, for Xpose 4

import.graph.par

Imports Xpose graphics settings from a file to an Xpose data object.

Column-transformation functions for Xpose 4

xpose.panel.splom

Scatterplot matrix panel function for Xpose 4

Population weighted residuals (WRES) plotted against the independent variable (IDV) for Xpose 4

iwres.dist.hist

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

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.

Observations (DV), individual predictions (IPRED) and population predictions (PRED) are plotted against the independent variable for every individual in the dataset, for Xpose 4

Observations (DV) plotted against individual predictions (IPRED) for Xpose 4

Plot scatterplot matrices of parameters, random parameters or covariates

Function to create a histogram of results from the randomization test tool (randtest) in http://psn.sf.net{PsN}

ind.plots.wres.qq

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

xpose4specific-internal

Internal xpose4specific Functions

Structured goodness of fit diagnostics.

xpose.plot.default

The Xpose 4 generic functions for continuous y-variables.

xpose.create.title.text

Create Xpose title text for plots.

export.graph.par

Exports Xpose graphics settings to a file.

xpose4specific-package

Xpose specific functions for a single purpose

Visual Predictive Check (VPC) using XPOSE

internal.functions

Internal functions for the VPC

Box-and-whisker plot of weighted residuals vs the independent variable for Xpose 4

xp.inc.prob.comb.2

Inclusion frequency plot for combination of covariates.

Resets Xpose variable definitions to factory settings

Extract or set the value of the Nsim slot.

Histogram of weighted residuals (WRES), for Xpose 4

Create a new graphical device for an Xpose plot.

Default box-and-whisker panel function for Xpose 4

xpose.ask.for.filename

Function to ask the user for the name of a file

print.xpose.multiple.plot

Print an Xpose multiple plot object.

The generic Xpose functions for box-and-whisker plots

xp.incl.index.cov

Plot of inclusion index of covariates.

xp.incl.index.cov.comp

Inclusion index individuals, compare between covariates.

xpose4psn-package

Xpose PsN post-processing functions

The generic Xpose functions for QQ plots

wres.vs.pred.bw

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

xpose.license.citation

Displays the Xpose license and citation information

xpose4classic-package

Xpose classic menu system

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

Summarize individual parameter values and covariates

xpose.multiple.plot.default

Xpose 4 generic function for plotting multiple lattice objects on one page

xpose4classic-internal

Internal xpose4classic Functions

xpose4data-internal

Internal xpose4data Functions

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

OFV difference (optimism) plot.

xpose4generic-package

Xpose generic multi-purpose functions

The Xpose Package

Generic table functions for Xpose 4

xpose.string.print

Print a pretty string.

Extracts and set Xpose variable definitions.

xpose4data-package

Xpose database creation and manipulation

xpose.panel.default

Default panel function for Xpose 4

absval.cwres.vs.pred

Absolute population conditional weighted residuals vs population predictions for Xpose 4

absval.iwres.vs.ipred.by.cov

Absolute individual weighted residuals vs individual predictions, conditioned on covariates, for Xpose 4

absval.wres.vs.pred.by.cov

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

absval.wres.vs.cov.bw

Absolute weighted residuals vs covariates for Xpose 4

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

ind.plots.wres.hist

Histograms of weighted residuals for each individual in an Xpose data object, for Xpose 4

Function to plot the coverage of the Numerical Predictive Check

Population weighted residuals (WRES) plotted against population predictions (PRED) for Xpose 4

xp.incl.index.cov.ind

Individual inclusion index

Function to create files for the simulated Prazosin example in Xpose

xpose.panel.histogram

Default histogram panel function for Xpose 4

xpose.prefs-class

Class "xpose.prefs"

dv.vs.pred.by.cov

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

Extract data from an xpose.data object.

Quantile-quantile plot of conditional weighted residuals (CWRES), for Xpose 4

dv.vs.pred.by.idv

Dependent variable vs population predictions, conditioned on independent variable, for Xpose 4

Classic menu functions for Xpose 4

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

Print run summary in Xpose 4

Quantile-quantile plot of weighted residuals (WRES), for Xpose 4

Inclusion frequency plot

Weighted residuals (WRES) plotted against covariates, for Xpose 4

Individual predictions (IPRED) plotted against the independent variable (IDV) for Xpose 4

xpose.multiple.plot

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

xpose.plot.splom

The Xpose 4 generic functions for scatterplot matrices.

xpose.plot.histogram

The Xpose 4 generic functions for continuous y-variables.