Extract sections of Nonmem control streams

This is a very commonly used wrapper for the input part of the model file. Look NMextractText for more general functionality suitable for the results part too.

NMreadSection(
  file = NULL,
  lines = NULL,
  text = NULL,
  section,
  return = "text",
  keep.empty = FALSE,
  keep.name = TRUE,
  keep.comments = TRUE,
  as.one = TRUE,
  clean.spaces = FALSE,
  simplify = TRUE,
  keepEmpty,
  keepName,
  keepComments,
  asOne,
  ...
)

NMgetSection(...)

Arguments

file

A file path to read from. Normally a .mod or .lst. See lines also.

lines

Text lines to process. This is an alternative to using the file argument.

text

Use this argument if the text to process is one long character string, and indicate the line separator with the linesep argument (handled by NMextractText). Use only one of file, lines, and text.

section

The name of section to extract without "$". Examples: "INPUT", "PK", "TABLE", etc. Not case sensitive.

return

If "text", plain text lines are returned. If "idx", matching line numbers are returned. "text" is default.

keep.empty

Keep empty lines in output? Default is FALSE. Notice, comments are removed before empty lines are handled if `keep.comments=TRUE`.

keep.name

Keep the section name in output (say, "$PROBLEM") Default is FALSE. It can only be FALSE, if return="text".

keep.comments

Default is to keep comments. If FALSE, the will be removed. See keep.empty too. Notice, there is no way for NMreadSection to keep comments and also drop lines that only contain comments.

as.one

If multiple hits, concatenate into one. This will most often be relevant with name="TABLE". If FALSE, a list will be returned, each element representing a table. Default is TRUE. So if you want to process the tables separately, you probably want FALSE here.

clean.spaces

If TRUE, leading and trailing are removed, and multiplied succeeding white spaces are reduced to single white spaces.

simplify

If asOne=FALSE, do you want the result to be simplified if only one section is found? Default is TRUE which is desirable for interactive analysis. For programming, you probably want FALSE.

keepEmpty

Deprecated. See keep.empty.

keepName

Deprecated. See keep.name.

keepComments

Deprecated. See keep.comments.

asOne

Deprecated. See as.one.

...

Additional arguments passed to NMextractText

Value

character vector with extracted lines.

character vector with extracted lines.

Functions

• NMgetSection: Deprecated function name. Use NMreadSection.

See also

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

Examples

NMreadSection(system.file("examples/nonmem/xgxr001.lst", package="NMdata"),section="DATA")
#> [1] "$DATA      xgxr1.csv IGNORE=@ IGNORE=(FLAG.NE.0)"