# Normalised Prediction Distribution Errors for Nonlinear Mixed-Effect Models

## Documentation for package ‘npde’ version 3.3

- DESCRIPTION file.

## Help Pages

A C D G K N P R S T V W misc

npde-package | Normalised prediction distribution errors for nonlinear mixed-effect models

## -- A --

autonpde | Compute normalised prediction distribution errors
aux.npdeplot.boxcov | Covariate diagnostic plots
aux.npdeplot.computepi | Scatterplots and VPC
aux.npdeplot.dist | Distribution plots of pd/npde
aux.npdeplot.hist | Distribution plots of pd/npde
aux.npdeplot.meanprof | Scatterplots and VPC
aux.npdeplot.pimat | Scatterplots and VPC
aux.npdeplot.transformObs | Scatterplots and VPC
aux.npdeplot.transformPI | Scatterplots and VPC

## -- C --

calcnpde.sim | Compute distribution of pd/npde using simulations
check.control.options | Set options for an NpdeObject
compute.bands | Scatterplots and VPC
compute.bands.true | Scatterplots and VPC
computenpde.loq | Method used to handle censored data
computenpde.omit | Method used to handle censored data

## -- D --

decorr.chol | Decorrelation methods in npde
decorr.inverse | Decorrelation methods in npde
decorr.polar | Decorrelation methods in npde
dist.pred.sim | Compute distribution of pd/npde using simulations

## -- G --

gof.test | Goodness-of-fit tests for npde
gof.test.default | Goodness-of-fit tests for npde
gof.test.NpdeObject | Goodness-of-fit tests for npde
gof.test.NpdeRes | Goodness-of-fit tests for npde
gof.test.numeric | Goodness-of-fit tests for npde

## -- K --

kurtosis | Kurtosis

## -- N --

npde | Compute normalised prediction distribution errors
npde.binning | Internal functions used to produce prediction intervals
npde.cens.method | Method used to handle censored data
npde.decorr.method | Decorrelation methods in npde
npde.graphs | Save the graphs for a NpdeObject object to a file
npde.graphs,NpdeObject | Class "NpdeObject"
npde.graphs-method | Save the graphs for a NpdeObject object to a file
npde.main,NpdeObject | Class "NpdeObject"
npde.plot.covariate | Covariate diagnostic plots
npde.plot.data | Plot a NpdeData object
npde.plot.default | Diagnostic plots
npde.plot.dist | Distribution plots of pd/npde
npde.plot.loq | Plot of the probability that the observations are below the LOQ
npde.plot.npd | Plots for pd and npde
npde.plot.npde | Plots for pd and npde
npde.plot.pd | Plots for pd and npde
npde.plot.scatterplot | Scatterplots and VPC
npde.plot.select | Select plot for a NpdeObject object
npde.plot.splitcov | Plots split by covariate for a NpdeObject object
npde.qqplot-method | Class "NpdeData" representing the structure of the longitudinal data
npde.save | Save the results contained in a NpdeObject object to a file
npde.save,NpdeObject | Class "NpdeObject"
npde.save-method | Save the results contained in a NpdeObject object to a file
npdeControl | Set options for an NpdeObject
NpdeData | Class "NpdeData" representing the structure of the longitudinal data
npdeData | Creates a NpdeData object
NpdeData-class | Class "NpdeData" representing the structure of the longitudinal data
NpdeObject | Class "NpdeObject"
NpdeObject-class | Class "NpdeObject"
NpdeSimData | Class "NpdeSimData" representing the structure of the longitudinal data
npdeSimData | Creates a NpdeSimData object
NpdeSimData-class | Class "NpdeSimData" representing the structure of the longitudinal data

## -- P --

plot | Diagnostic plots
plot,NpdeObject | Class "NpdeObject"
plot.npde | Plots a NpdeObject object
plot.NpdeData | Plots a NpdeData object
plot.NpdeObject | Plots a NpdeObject object
plotNpde | Plots a NpdeObject object
print-method | Class "NpdeData" representing the structure of the longitudinal data
print-method | Class "NpdeObject"
print.NpdeData | Prints objects from the npde package
print.NpdeObject | Prints objects from the npde package
print.NpdeRes | Prints objects from the npde package
printgoftest | Goodness-of-fit tests for npde

## -- R --

replace.control.options | Set options for an NpdeObject

## -- S --

set.plotoptions | Set graphical preferences
set.plotoptions-method | Set graphical preferences
set.plotoptions.default | Set graphical preferences
set.plotoptions.NpdeData | Set graphical preferences
set.plotoptions.NpdeObject | Set graphical preferences
show | Displays npde objects
show-method | Displays npde objects
show.NpdeData | Displays npde objects
show.NpdeObject | Displays npde objects
show.NpdeRes | Displays npde objects
show.NpdeSimData | Displays npde objects
showall | Contents of an object
showall,method | Contents of an object
showall-method | Class "NpdeObject"
showall-method | Contents of an object
showall.default | Contents of an object
showall.NpdeData | Contents of an object
showall.NpdeObject | Contents of an object
showall.NpdeRes | Contents of an object
simtheopp | Simulated data for the computation of normalised prediction distribution errors in the theophylline dataset
simvirload | Simulated HIV viral loads in HIV patients
simwarfarinBase | Pharmacokinetics of warfarin
simwarfarinCov | Pharmacokinetics of warfarin
skewness | Skewness
subset.NpdeData | Subsetting a NpdeData object
subset.NpdeObject | Subsetting a NpdeData object
summary-method | Class "NpdeData" representing the structure of the longitudinal data
summary-method | Class "NpdeObject"
summary.NpdeData | Summary of a NpdeData object
summary.NpdeObject | Summary of a NpdeData object
summary.NpdeRes | Summary of a NpdeData object

## -- T --

test-method | Class "NpdeObject"
theopp | Pharmacokinetics of theophylline

## -- V --

virload | Simulated HIV viral loads in HIV patients
virload20 | Simulated HIV viral loads in HIV patients
virload50 | Simulated HIV viral loads in HIV patients
virloadMDV20 | Simulated HIV viral loads in HIV patients

## -- W --

warfarin | Pharmacokinetics of warfarin

## -- misc --

[ | Get/set methods for NpdeData object
[,NpdeSimData | Get/set methods for NpdeData object
[-method | Get/set methods for NpdeData object
[<-,NpdeSimData | Get/set methods for NpdeData object
[<--method | Get/set methods for NpdeData object