Package: nonmem2R 0.2.5

Magnus Astrand

nonmem2R: Loading NONMEM Output Files with Functions for Visual Predictive Checks (VPC) and Goodness of Fit (GOF) Plots

Loading NONMEM (NONlinear Mixed-Effect Modeling, <https://www.iconplc.com/solutions/technologies/nonmem/>) and PSN (Perl-speaks-NONMEM, <https://uupharmacometrics.github.io/PsN/>) output files to extract parameter estimates, provide visual predictive check (VPC) and goodness of fit (GOF) plots, and simulate with parameter uncertainty.

Authors:Magnus Astrand

nonmem2R_0.2.5.tar.gz
nonmem2R_0.2.5.tar.gz(r-4.7-any)nonmem2R_0.2.5.tar.gz(r-4.6-any)
nonmem2R_0.2.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nonmem2R/json (API)

# Install 'nonmem2R' in R:
install.packages('nonmem2R', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

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

3.23 score 3 stars 28 scripts 474 downloads 1 mentions 61 exports 35 dependencies

Last updated from:4c335a398c. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK159
source / vignettesOK203
linux-release-x86_64OK166
wasm-releaseOK165

Exports:add.captionbasic.eta.GOFbasic.GOF4basic.GOF6covloadcovload.sub.tabledefault.GOF.dictionarydefault.GOF.paramsdo.cat.GOFdo.individual.GOFdo.multi.GOFdo.one.GOFeta.cat.GOFeta.cov.GOFeta.hist.GOFeta.pairs.GOFeta.qqnorm.GOFextFormatextloadextload.sub.tableextToTableextTransformget.GOF.dictionaryget.GOF.paramsget.labelget.model.pathGOF.controlgrid.simgrid.sim.internal1grid.sim.internal2grid.sim.internal3histGOFmerge2GOFmerge4GOFmerge6GOFmodloadposition_scalePositionScaleqqnormGOFreadVpcset.ETA.labelsset.GOF.dictionaryset.GOF.paramsset.model.pathset.script.namestat_corrstat_denxstat_dnormstat_hmeanstat_hmedianStatCorrStatDenxStatDnormStatHmeanStatHmediansumoRsumoRUtest.grid.simvpcfigvpcfig2vpcfig3

Dependencies:clicpp11deldirfarverggplot2gluegridExtragtableinterpisobandjpeglabelinglatticelatticeExtralifecyclemagrittrMASSmvtnormplyrpngR6RColorBrewerRcppRcppArmadilloRcppEigenreshape2rlangS7scalessplines2stringistringrvctrsviridisLitewithr

nonmem2R VPC plot functions
Introduction | vpcfig2 | Adding ggplot formating | Using the fy argument for logarithmic scale | Re-naming, subsetting and or re-order of strata's | VPC for BLQ data
Rendered fromVPCvignette.Rmdusingknitr::rmarkdown

Last update: 2020-09-28
Started: 2020-09-28

nonmem2R goodness of fit plot functions
Introduction | Functions | Tailored GOF functions | Labels and formatting options | Labels | Formatting with set.GOF.params | GOF building block's | GOF builders
Rendered fromGOFvignette.Rmdusingknitr::rmarkdown

Last update: 2019-02-18
Started: 2019-02-18

Readme and manuals

Help Manual

Help pageTopics
Add caption to ggplot objectadd.caption
Histogram and/or QQ-norm GOF for ETA'sbasic.eta.GOF eta.hist.GOF eta.qqnorm.GOF
Basic 4- and 6-panel GOFbasic.GOF4 basic.GOF6
Load the covariance matrix from a nonmem .cov output file.covload
Y vs categorical X GOF-plotdo.cat.GOF
Individual GOF-plotsdo.individual.GOF
Multiple Y vs single X GOF-plotdo.multi.GOF
X-Y GOF-plotdo.one.GOF
Covariate and pairs ETA GOFseta.cat.GOF eta.cov.GOF eta.pairs.GOF
Load final parameter values from a nonmem .ext output file.extload
Compile parameter table suitable for reportsextToTable
Get, set, and modify the global (or local) GOF parameters and GOF dictionary for labelsdefault.GOF.dictionary default.GOF.params get.GOF.dictionary get.GOF.params GOF.control set.ETA.labels set.GOF.dictionary set.GOF.params set.script.name
Labels for known NONMEM variablesget.label
Get and set model.pathget.model.path set.model.path
Combine fix grid and simulated grid based on multivariate normal distributiongrid.sim
Histogram GOFhistGOF
Merging 2, 4, or 6 GOF's into one graphmerge2GOF merge4GOF merge6GOF
Show model filemodload
Position for scaling yposition_scale
QQ-norm GOFqqnormGOF
Adding correlation to x-y plotsstat_corr
Density for x in x-y plotstat_denx
Normal densitystat_dnorm
Horizontal reference at meanstat_hmean
Horizontal reference at medianstat_hmedian
Compile summary information for NONMEM model based on the lst file, ext file, and the cov file.sumoR
Function for testing grid.sim and compare with rmvnormtest.grid.sim
Visual Predictive Check (VPC) based on Perl-speaks-NONMEM (PsN) generated VPC files (lattice version).vpcfig
Visual Predictive Check (VPC) based on Perl-speaks-NONMEM (PsN) generated VPC files (ggplot2-version).vpcfig2
Visual Predictive Check (VPC) based on raw Perl-speaks-NONMEM (PsN) generated VPC files.vpcfig3