nm.pl: Build Commands to Invoke NONMEM

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

Description

Format a set of commandlines, suitable for submission to a command shell, to operate the executable for an NMQual-mediated NONMEM installation. nm.pl is the default for NONMEM 7.1.2 and earlier. autolog.pl is the default for NONMEM 7.2.0 and later.

Usage

nm.pl(
	command,
	ctlfile,
	outfile = NULL,
	perl = 'perl',
	checksum = TRUE,
	compile = TRUE, 
	execute = TRUE,
	split = FALSE,
	...
)
autolog.pl(
	command, 
	rdir, 
	run, 
	perl = "perl", 
	compile = TRUE, 
	execute = TRUE, 
	split = FALSE,
	config = file.path(dirname(command),"log.xml"),
	mode = "run", 
	...
)

Arguments

command	path for the installation-specific variant of ‘nm.pl’
ctlfile	path for a control stream
outfile	path for output
perl	how to invoke Perl on this system
checksum	whether to conduct checksums
compile	whether to compile NONMEM
execute	whether to execute the compiled NONMEM
split	whether to compile and execute as separate steps
rdir	run directory
run	run name
config	path to a configuration file (sensu NMQual 8)
mode	process mode
...	ignored

Details

If split is TRUE, two commands are returned, having the mode flags ‘c’ and ‘e’, respectively. nm.pl drops the ‘c’ or ‘e’ argument if split is FALSE and both compile and execute are TRUE. In the identical case, autolog.pl passes ‘ce’.

autolog.pl returns a run directory and run name, rather than input and output file paths as in nm.pl. autolog.pl does not support checksum. By default, autolog.pl expects a config file called ‘log.xml’ in the same directory as command; it also assumes the mode is ‘run’. See also http://nmqual.googlecode.com.

Value

character

Author(s)

Tim Bergsma

References

http://metrumrg.googlecode.com

See Also

• runCommand

Examples

nm.pl('/nm6/test/nm6.pl','1.ctl')
nm.pl('/nm6/test/nm6.pl','1.ctl','1.out',checksum=FALSE)
nm.pl('/nm6/test/nm6.pl','1.ctl',execute=FALSE)
nm.pl('/nm6/test/nm6.pl','1.ctl',compile=FALSE)
nm.pl('/nm6/test/nm6.pl','1.ctl',split=TRUE)
autolog.pl('/nm72/nmqual/autolog.pl','/home/ubuntu/test/3',3)

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