runlog: Convert Model Metadata to Various Formats

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

Description

Metadata from successful model runs, e.g. NONMEM, comes in various formats, some of which are version dependent. NONMEM6 and 7 outputs are interconverted with support for the conventional run log format as well as a universal format.

Usage

runlog()
unilog()
as.runlog.file(file, ...)
as.unilog.lst(file, run, tool, ...)
as.unilog.pxml(x, run, tool = 'nm7', ...)
as.unilog.runlog(x, tool = 'nm6', ...)
as.runlog.unilog(x, ...)
as.file.runlog(x, file = 'NonmemRunLog.csv', header = FALSE, quote = FALSE, na = '.', ...)

Arguments

x	data.frame in runlog or unilog format
file	file name for metadata file, e.g. ‘NonmemRunLog.csv’, ‘3.lst’
header	whether to include column names in output
quote	whether to quote cell contents
na	string to represent NA in output
...	passed arguments
run	name (number) of the model run corresponding to the data
tool	the tool that created the metadata: currently ‘nm6’ or ‘nm7’

Details

These functions are not typically needed by the user, since rlog serves as an interface.

Metadata may reside in ‘lst’ files (NONMEM primary output), in ‘NonmemRunLog’ files (created for NONMEM6 by metrumrg INFN routine) or in ‘ext’ files (NONMEM7 secondary output). as.unilog.lst, as.runlog.file, and as.pxml.ext (documented elsewhere) read these formats. pxml is an internal xml format produced by as.pxml.ext and converted to unilog by as.unilog.pxml.

The runlog format by convention has the columns: prob, moment, min, cov, mvof, p1...pn, and (possibly) run. p1 through pn are (an arbitrary number of) parameters for that run. The others give, respectively, the problem statement, a flag to identify relative standard error percent, minimization status, covariance status, minimum value of the objective function, and run name (number). The primary values for each variable are given in a single record. Where available, a second record gives ‘PRSE’, with non-informative entries as necessary. Usually the header is not present in files.

The unilog format is fully normalized. It has the columns: tool, run, parameter, moment, value. Moment is, for instance, ‘estimate’ or ‘prse’. Typically all cells are filled and meaningful. The value column is handled as text for maximum compatibility across data types. The term ‘parameter’ is used informally: several items typically captured are not really parameters per se.

Unilog and runlog formats are interconvertible via as.runlog.unilog and as.unilog.runlog. as.file.runlog creates the traditional disk file from the runlog format; writing unilog to disk is left to conventional strategies.

runlog and unilog return zero-row data.frames with the corresponding formats.

Value

as.file.runlog is used for side effects. All others return data.frame in the runlog or unilog format.

Note

These functions are not vectorized: their first arguments are expected to represent a single model run.

As of 5.18, as.unilog.run tries to give a more meaningful value of 'min' than just 1 or 0 for NONMEM 7. Not supported on NONMEM 7.1.2, since it requires the .xml file available under 7.2.

Author(s)

Tim Bergsma

References

http://metrumrg.googlecode.com

See Also

• as.unilog.run

• rlog

• as.pxml.ext

Examples

runlog()
unilog()
ext <- c(
	'TABLE NO.  1: First Order: Goal Function=MINIMUM VALUE OF OBJECTIVE FUNCTION',
	' ITERATION    THETA1       THETA2       THETA3       SIGMA(1,1)   OMEGA(1,1)   OBJ',
	'            0  1.70E+0  1.02E-1  2.90E+1  0.00E+0  1.17E+0  11.570086639848398',
	'            2  1.78E+0  1.06E-1  3.05E+1  0.00E+0  1.08E+0  9.377909428896904',
	'            4  1.91E+0  1.05E-1  3.14E+1  0.00E+0  8.96E-1  8.983605357031118',
	'            6  1.94E+0  1.01E-1  3.20E+1  0.00E+0  9.06E-1  8.940731060922468',
	'            8  1.93E+0  1.01E-1  3.20E+1  0.00E+0  8.99E-1  8.940110966224346',
	'           10  1.94E+0  1.01E-1  3.20E+1  0.00E+0  8.99E-1  8.940101673144566',
	'           11  1.94E+0  1.01E-1  3.20E+1  0.00E+0  8.99E-1  8.940101673144566',
	'  -1000000000  1.94E+0  1.01E-1  3.20E+1  0.00E+0  8.99E-1  8.940101673144566',
	'  -1000000001  6.28E-1  7.36E-3  1.25E+0  0.00E+0  5.44E-1  0.'
)
file <- textConnection(ext)
pxml <- as.pxml.ext(file)
close(file)
pxml
unip <- as.unilog.pxml(pxml,run=3)
unip
runlogfile <- c(
'1001  2 compartment base,,  0,  1,  0.1439E+5,  0.2E+1,  0.4E+1,  0.2E+1,  0.5E+1,  
0.1E+1,  0.0E+0,  0.0E+0,  0.0E+0,  0.0E+0,  0.0E+0,  0.1E+0,  0.0E+0,  0.0E+0,  
0.0E+0,  0.0E+0,  0.0E+0,  0.0E+0,  0.0E+0,  0.0E+0,  0.0E+0,  0.0E+0,  0.0E+0,  
0.0E+0,  0.0E+0,  0.0E+0,  0.3E+0,  0.1E+1,  0.0E+0,  0.0E+0, ,',
'1001  2 compartment base,RSE,,,,0,0,0,0,0,0,0,0,0,0,  0.0E+0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,  0.0E+0,  0.0E+0,0,0, ,'
)
runlogfile <- sub('\n','',runlogfile)
file <- textConnection(runlogfile)
rlg  <- as.runlog.file(file)
close(file)
rlg
as.runlog.unilog(unip)
as.unilog.runlog(rlg)

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