nm.extract.xml: NONMEM output extraction from XML output

In qPharmetra/qpToolkit: qPharmetra R Tools

NONMEM output extraction from XML output

Description

Extracts all output embedded in the XML file of a NONMEM run

Usage

nm.extract.xml(
  run = "run1",
  path = getOption("nmDir"),
  filename = paste(path, run, paste(run, xml.extension, sep = ""), sep = "/"),
  digits = 3,
  digits.se = digits,
  digits.cv = digits,
  digits.est = digits,
  xml.extension = ".xml",
  zip.extension = ".7z",
  zip.call = getOption("unzip.call"),
  remove.obsolete = FALSE,
  na.value = "n.d.",
  control_stream = FALSE,
  get.xpose.tables = TRUE,
  quiet = TRUE
)

Arguments

run	run rootname (e.g. run1)
path	directory where run resides
filename	with full path of the XML file to be parsed. This is automatically created using qP workflow standards but can be specified as well
digits	number of significant digits
digits.se	number of significant digits in SE (when point estimates = T)
digits.cv	number of significant digits in CV% (when point.estimates = T)
digits.est	number of significant digits in parameter estimates (when point.estimates = T)
xml.extension	extension of the xml file. Defaults to ".xml"
zip.extension	extension of the zip program. Defaults to ".7z"
zip.call	full OS call to zip utility for unzipping. Defaults to "c:/progra~1/7-zip/7z e %s.7z" on windows
remove.obsolete	logical (F) defining if non-estimated parameters should be dropped for the parameter table.
na.value	what to do with an NA value in the parameter table. Defaults to "n.d."
control_stream	logical (F) defining if the control stream should be included as well.
get.xpose.tables	logical (T) defining if the xpose tables should be integrated in the result as a single data frame using the function get.xpose.tables
quiet	if TRUE (default) silences any message returned by the function and subfunctions.

Value

An extensive list with all elements extracted from the XML output

Note

Works for NM7.2 (up to 9 OMEGAs) and NM7.3 (bug free)

Examples

tmp = nm.extract.xml("example2", path = getOption("qpExampleDir"))
names(tmp)
tmp$final_objective_function
tmp$table
tmp$monitor
tmp = nm.extract.xml("example2", path = getOption("qpExampleDir"))

qPharmetra/qpToolkit documentation built on May 24, 2023, 8:52 a.m.