devel/movedToNMdata/NMgetSection.R

In philipdelff/pmxtricks: Every-day pharmacometrics helper functions

##' 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.
##'
##' @param file A file to read from. Normally a .mod or .lst. See
##'     lines also.
##' @param lines Text lines to process. This is an alternative to use
##'     the file argument.
##' @param text Use this argument if the text to process is one long
##'     character string, and indicate the line seperator with the
##'     linesep argument (handled by NMextractText). Use only one of
##'     file, lines, and text.
##' @param section The name of section to extract. Examples: "INPUT",
##'     "PK", "TABLE", etc.
##' @param return If "text", plain text lines are returned. If "idx",
##'     matching line numbers are returned. "text" is default.
##' @param keepEmpty Keep empty lines in output? Default is FALSE.
##' @param keepName Keep the section name in output (say, "$PROBLEM")
##'     Default is TRUE. It can only be FALSE, if return"idx".
##' @param keepComments Keep comment lines?
##' @param asOne 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.
##' @param simplify If asOne=FALSE, do you want the result to be
##'     simplified if only one table is found? Default is TRUE which
##'     is desirable for interactive analysis. For programming, you
##'     probably want FALSE.
##' @param cleanSpaces If TRUE, leading and trailing are removed, and
##'     multiplied succeeding white spaces are reduced to single white
##'     spaces.
##' @param debug Start by calling browser()?
##' @param ... Additional arguments passed to NMextractText
##' @family Nonmem
##' @examples
##' NMgetSection(pmxtricks_filepath("examples/nonmem/run001.lst"),section="DATA")



NMgetSection <- function(file=NULL, lines=NULL, text=NULL, section, return="text", keepEmpty=FALSE, keepName=TRUE, keepComments=TRUE, asOne=TRUE, simplify=TRUE, cleanSpaces=FALSE, debug=F, ...){

    NMextractText(file=file, lines=lines, text=text, section=section,
                  ## this wrapper is especially made for "$" sections
                  char.section="\\$",
                  return=return,
                  keepEmpty=keepEmpty,
                  keepName=keepName,
                  keepComments=keepComments,
                  asOne=asOne,
                  simplify=simplify,
                  cleanSpaces=cleanSpaces,
                  ## we only consider the model definition, not results.
                  type="mod",
                  debug=debug,
                  ...)
    
}