Package: npde 3.5

npde: Normalised Prediction Distribution Errors for Nonlinear Mixed-Effect Models

Provides routines to compute normalised prediction distribution errors, a metric designed to evaluate non-linear mixed effect models such as those used in pharmacokinetics and pharmacodynamics.

Authors:Emmanuelle Comets [aut, cre], Karl Brendel [ctb], Thi Huyen Tram Nguyen [ctb], Marc Cerou [ctb], Romain Leroux [ctb], France Mentre [ctb]

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npde.pdf |npde.html
npde/json (API)

# Install 'npde' in R:
install.packages('npde', repos = c('https://ecomets.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • simtheopp - Simulated data for the computation of normalised prediction distribution errors in the theophylline dataset
  • simvirload - Simulated HIV viral loads in HIV patients
  • simwarfarinCov - Pharmacokinetics of warfarin
  • theopp - Pharmacokinetics of theophylline
  • 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
  • warfarin - Pharmacokinetics of warfarin

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

30 exports 3.62 score 30 dependencies 6 dependents 2 mentions 117 scripts 690 downloads

Last updated 8 months agofrom:31f075e207. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 14 2024
R-4.5-winOKSep 14 2024
R-4.5-linuxOKSep 14 2024
R-4.4-winOKSep 14 2024
R-4.4-macOKSep 14 2024
R-4.3-winOKSep 14 2024
R-4.3-macOKSep 14 2024

Exports:autonpdecheck.control.optionsdist.pred.simgof.testkurtosisnpdenpde.binningnpde.graphsnpde.plot.covariatenpde.plot.datanpde.plot.defaultnpde.plot.distnpde.plot.loqnpde.plot.npdnpde.plot.npdenpde.plot.pdnpde.plot.scatterplotnpde.plot.selectnpde.plot.splitcovnpde.savenpdeControlnpdeDatanpdeSimDataprintgoftestreadreplace.control.optionsset.plotoptionsshowshowallskewness

Dependencies:clicolorspacefansifarverggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmclustmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Normalised prediction distribution errors for nonlinear mixed-effect modelsnpde-package
Get/set methods for NpdeData object[ [,NpdeData-method [,NpdeObject-method [,NpdeRes-method [,NpdeSimData [,NpdeSimData-method [<-,NpdeData-method [<-,NpdeObject-method [<-,NpdeRes-method [<-,NpdeSimData [<-,NpdeSimData-method
Compute normalised prediction distribution errorsautonpde npde
Compute distribution of pd/npde using simulationscalcnpde.sim dist.pred.sim
Goodness-of-fit tests for npdegof.test gof.test.default gof.test.NpdeObject gof.test.NpdeRes gof.test.numeric printgoftest
Kurtosiskurtosis
Internal functions used to produce prediction intervalsnpde.binning
Method used to handle censored datacomputenpde.loq computenpde.omit npde.cens.method
Decorrelation methods in npdedecorr.chol decorr.inverse decorr.polar npde.decorr.method
Save the graphs for a NpdeObject object to a filenpde.graphs npde.graphs,NpdeObject-method
Covariate diagnostic plotsaux.npdeplot.boxcov npde.plot.covariate
Plot a NpdeData objectnpde.plot.data
Diagnostic plotsnpde.plot.default plot
Distribution plots of pd/npdeaux.npdeplot.dist aux.npdeplot.hist npde.plot.dist
Plot of the probability that the observations are below the LOQnpde.plot.loq
Plots for pd and npdenpde.plot.npd npde.plot.npde npde.plot.pd
Scatterplots and VPCaux.npdeplot.computepi aux.npdeplot.meanprof aux.npdeplot.pimat aux.npdeplot.transformObs aux.npdeplot.transformPI compute.bands compute.bands.true npde.plot.scatterplot
Select plot for a NpdeObject objectnpde.plot.select
Plots split by covariate for a NpdeObject objectnpde.plot.splitcov
Save the results contained in a NpdeObject object to a filenpde.save npde.save,NpdeObject-method
Set options for an NpdeObjectcheck.control.options npdeControl replace.control.options
Creates a NpdeData objectnpdeData
Class "NpdeData" representing the structure of the longitudinal datanpde.qqplot,NpdeData-method NpdeData NpdeData-class print,NpdeData-method summary,NpdeData-method
Class "NpdeObject"npde.graphs,NpdeObject npde.main,NpdeObject npde.save,NpdeObject NpdeObject NpdeObject-class plot,NpdeObject print,NpdeObject-method showall,NpdeObject-method summary,NpdeObject-method test,NpdeObject-method
Creates a NpdeSimData objectnpdeSimData
Class "NpdeSimData" representing the structure of the longitudinal dataNpdeSimData NpdeSimData-class
Plots a NpdeData objectplot.NpdeData
Plots a NpdeObject objectplot.npde plot.NpdeObject plotNpde
Prints objects from the npde packageprint.NpdeData print.NpdeObject print.NpdeRes
Set graphical preferencesset.plotoptions set.plotoptions,NpdeData-method set.plotoptions,NpdeObject-method set.plotoptions.default set.plotoptions.NpdeData set.plotoptions.NpdeObject
Displays npde objectsshow show,NpdeData-method show,NpdeObject-method show,NpdeRes-method show,NpdeSimData-method show,Object-method show.NpdeData show.NpdeObject show.NpdeRes show.NpdeSimData
Contents of an objectshowall showall,method showall,NpdeData-method showall.default showall.NpdeData showall.NpdeObject showall.NpdeRes
Simulated data for the computation of normalised prediction distribution errors in the theophylline datasetsimtheopp
Skewnessskewness
Subsetting a NpdeData objectsubset.NpdeData subset.NpdeObject
Summary of a NpdeData objectsummary.NpdeData summary.NpdeObject summary.NpdeRes
Pharmacokinetics of theophyllinetheopp
Simulated HIV viral loads in HIV patientssimvirload virload virload20 virload50 virloadMDV20
Pharmacokinetics of warfarinsimwarfarinBase simwarfarinCov warfarin