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nonmem2R (version 0.2.5)

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

Description

Loading NONMEM (NONlinear Mixed-Effect Modeling, ) and PSN (Perl-speaks-NONMEM, ) output files to extract parameter estimates, provide visual predictive check (VPC) and goodness of fit (GOF) plots, and simulate with parameter uncertainty.

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Version

Install

install.packages('nonmem2R')

Monthly Downloads

496

Version

0.2.5

License

Unlimited

Maintainer

Magnus Astrand

Last Published

March 11th, 2024

Functions in nonmem2R (0.2.5)

do.one.GOF

X-Y GOF-plot
do.individual.GOF

Individual GOF-plots
readVpc

Internal package function
stat_corr

Adding correlation to x-y plots
merge2GOF

Merging 2, 4, or 6 GOF's into one graph
position_scale

Position for scaling y
histGOF

Histogram GOF
modload

Show model file
get.model.path

Get and set model.path
do.multi.GOF

Multiple Y vs single X GOF-plot
get.label

Labels for known NONMEM variables
extFormat

Internal package function
extToTable

Compile parameter table suitable for reports
do.cat.GOF

Y vs categorical X GOF-plot
covload.sub.table

Internal package function
stat_hmean

Horizontal reference at mean
grid.sim

Combine fix grid and simulated grid based on multivariate normal distribution
stat_hmedian

Horizontal reference at median
qqnormGOF

QQ-norm GOF
print.sumoR

Print function for compiled summary information of class sumoR
sumoR

Compile summary information for NONMEM model based on the lst file, ext file, and the cov file.
extload.sub.table

Internal package function
get.GOF.dictionary

Get, set, and modify the global (or local) GOF parameters and GOF dictionary for labels
eta.cov.GOF

Covariate and pairs ETA GOFs
test.grid.sim

Function for testing grid.sim and compare with rmvnorm
stat_denx

Density for x in x-y plot
grid.sim.internal3

Internal function
vpcfig

Visual Predictive Check (VPC) based on Perl-speaks-NONMEM (PsN) generated VPC files (lattice version).
grid.sim.internal2

Internal function
grid.sim.internal1

Internal function
sumoRU

Internal package function
print.extToTable

Print function for compiled summary information of class extToTable
vpcfig2

Visual Predictive Check (VPC) based on Perl-speaks-NONMEM (PsN) generated VPC files (ggplot2-version).
print.modload

Print function for loaded mod file
vpcfig3

Visual Predictive Check (VPC) based on raw Perl-speaks-NONMEM (PsN) generated VPC files.
stat_dnorm

Normal density
StatCorr

ggproto for stat_corr
covload

Load the covariance matrix from a nonmem .cov output file.
add.caption

Add caption to ggplot object
basic.eta.GOF

Histogram and/or QQ-norm GOF for ETA's
basic.GOF4

Basic 4- and 6-panel GOF
extload

Load final parameter values from a nonmem .ext output file.
StatDenx

ggproto for stat_denx
PositionScale

ggproto for position_scale
StatDnorm

ggproto for stat_dnorm
StatHmedian

ggproto for stat_hmedian
StatHmean

ggproto for stat_hmean
extTransform

Internal package function