omegacor: Extract NONMEM Covariance or Correlation Matrices

In metrumrg: Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting

Description

These functions acquire omega or sigma covariance matrix elements for a NONMEM 7 run and return them as a matrix or calculate the corresponding correlation matrix. Arguments run and project are used to calculate the .ext file name, which is read into memory as a pxml object, and then converted to unilog format. Directly supplying extfile, pxml, or unilog renders all previous arguments moot. Not vectorized: run should be scalar.

Usage

unilogcov(
	pattern,
	run=0,
	project=getwd(),
	tool='nm7',
	extfile=file.path(project,run,paste(run,'ext',sep='.')),
	pxml=as.pxml.ext(extfile),
	unilog=as.unilog.pxml(x=pxml,run=run,tool=tool,...),
	...
)
unilogcor(
	pattern,
	run=0,
	project=getwd(),
	tool='nm7',
	extfile=file.path(project,run,paste(run,'ext',sep='.')),
	pxml=as.pxml.ext(extfile),
	unilog=as.unilog.pxml(x=pxml,run=run,tool=tool,...),
	...
)
omegacov(run,project=getwd(),...)
sigmacov(run,project=getwd(),...)
omegacor(run,project=getwd(),...)
sigmacor(run,project=getwd(),...)

Arguments

pattern	a pattern to seek in the parameter column of a unilog (anchored at the start of each string)
run	name (number) of a run
project	project directory (parent of run directory)
tool	largely irrelevant; only 'nm7' is supported
extfile	name of .ext file, e.g. run.ext
pxml	internal xml format for parameter data
unilog	unilog format; as returned invisibly by rlog
...	passed to unilogcor, else unused

Value

correlation matrix

Author(s)

Tim Bergsma

References

http://metrumrg.googlecode.com

See Also

• cov2cor

• rlog

metrumrg documentation built on May 2, 2019, 5:55 p.m.