NMwriteSection: Replace ($)sections of a Nonmem control stream

In NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling

Replace ($)sections of a Nonmem control stream

Description

Just give the section name, the new lines and the file path, and the "$section", and the input to Nonmem will be updated.

Usage

NMwriteSection(
  files,
  file.pattern,
  dir,
  section,
  newlines,
  list.sections,
  location = "replace",
  newfile,
  backup = TRUE,
  blank.append = TRUE,
  data.file,
  write = TRUE,
  quiet,
  simplify = TRUE
)

Arguments

files	File paths to the models (control stream) to edit. See file.pattern too.
file.pattern	Alternatively to files, you can supply a regular expression which will be passed to list.files as the pattern argument. If this is used, use dir argument as well. Also see data.file to only process models that use a specific data file.
dir	If file.pattern is used, dir is the directory to search in.
section	The name of the section to update with or without "$". Example: section="EST" or section="$EST" to edit the sections starting by $EST. Section specification is not case-sensitive. See ?NMreadSection too.
newlines	The new text (including "$SECTION"). Better be broken into lines in a character vector since this is simply past to writeLines.
list.sections	Named list of new sections, each element containing a section. Names must be section names, contents of each element are the new section lines for each section.
location	In combination with 'section', this determines where the new section is inserter. Possible values are "replace" (default), "before", "after", "first", "last".
newfile	path and filename to new run. If missing, the original file (from files or file.pattern) is overwritten (see the backup option below). If NULL, output is returned as a character vector rather than written.
backup	In case you are overwriting the old file, do you want to backup the file (to say, backup_run001.mod)?
blank.append	Append a blank line to output?
data.file	Use this to limit the scope of models to those that use a specific input data data file. The string has to exactly match the one in $DATA or $INFILE in Nonmem.
write	Default is to write to file. If write=FALSE, NMwriteSection returns the resulting input.txt without writing it. to disk? Default is FALSE.
quiet	The default is to give some information along the way on what data is found. But consider setting this to TRUE for non-interactive use. Default can be configured using NMdataConf.
simplify	If TRUE (default) and only one file is edited, the resulting rows are returned directly. If more than one file is edited, the result will always be a list with one element per file.

Details

The new file will be written with unix-style line endings.

Value

The new section text is returned. If write=TRUE, this is done invisibly.

See Also

Other Nonmem: NMapplyFilters(), NMextractText(), NMgenText(), NMreadSection(), NMreplaceDataFile()

Examples

newlines <- "$EST POSTHOC INTERACTION METHOD=1 NOABORT PRINT=5 MAXEVAL=9999 SIG=3"
NMwriteSection(files=system.file("examples/nonmem/xgxr001.mod", package = "NMdata"),
section="EST", newlines=newlines,newfile=NULL)
## Not run: 
text.nm <- NMwriteData(data)
NMwriteSection(dir="nonmem",
              file.pattern="^run.*\\.mod",
              list.sections=text.nm["INPUT"])

## End(Not run)

NMdata documentation built on Nov. 11, 2023, 5:07 p.m.