Generate text for INPUT and possibly DATA sections of NONMEM control streams.

The user is provided with text to use in Nonmem. NMwriteSection can use the results to update the control streams. INPUT lists names of the data columns while DATA provides a path to data and ACCEPT/IGNORE statements. Once a column is reached that Nonmem will not be able to read as a numeric and column is not in nm.drop, the list is stopped. Only exception is TIME which is not tested for whether character or not.

NMgenText(
  data,
  drop,
  col.flagn = "FLAG",
  rename,
  copy,
  file,
  dir.data,
  capitalize = FALSE,
  until,
  allow.char.TIME = TRUE,
  width,
  quiet
)

Arguments

data

The data that NONMEM will read.

drop

Only used for generation of proposed text for INPUT section. Columns to drop in Nonmem $INPUT. This has two implications. One is that the proposed $INPUT indicates =DROP after the given column names. The other that in case it is a non-numeric column, succeeding columns will still be included in $INPUT and can be read by NONMEM.

col.flagn

Name of a numeric column with zero value for rows to include in Nonmem run, non-zero for rows to skip. The argument is only used for generating the proposed $DATA text to paste into the Nonmem control stream. To skip this feature, use col.flagn=NULL. Default is defined by NMdataConf.

rename

For the $INPUT text proposal only. If you want to rename columns in NONMEM $DATA, NMwriteData can adjust the suggested $DATA text. If you plan to use BBW instead of BWBASE in Nonmem, consider rename=c(BBW="BWBASE"). The result will include BBW and not BWBASE.

copy

For the $INPUT text proposal only. If you plan to use additional names for columns in Nonmem $INPUT, NMwriteData can adjust the suggested $INPUT text. Say you plan to use CONC as DV in Nonmem, use copy=c(DV="CONC"), i.e. copy=c(newname="existing"). INPUT suggestion will in this case contain DV=CONC.

file

The file name NONMEM will read the data from (for the $DATA section). It can be a full path.

dir.data

For the $DATA text proposal only. The path to the input datafile to be used in the Nonmem $DATA section. Often, a relative path to the actual Nonmem run is wanted here. If this is used, only the file name and not the path from the file argument is used.

capitalize

For the $INPUT text proposal only. If TRUE, all column names in $INPUT text will be converted to capital letters.

until

Use this to truncate the columns in $INPUT. until can either be a character (column name) or a numeric (column number). If a character is given, it is matched against the resulting column name representation in $INPUT, i.e. this could be "DV=CONC" if you are using in this case the copy argument. In case until is of length>1, the maximum will be used (probably only interesting if character values are supplied).

allow.char.TIME

For the $INPUT text proposal only. Assume Nonmem can read TIME and DATE even if it can't be translated to numeric. This is necessary if using the 00:00 format. Default is TRUE.

width

If positive, will be passed to strwrap for the $INPUT text. If missing or NULL, strwrap will be called with default value. If negative or zero, strwrap will not be called.

quiet

Hold messages back? Default is defined by NMdataConf.

Value

Text for inclusion in Nonmem control stream, invisibly. A list with elements `DATA` and `INPUT`.

See also

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