NMgenText | R Documentation |
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
)
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 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. |
Text for inclusion in Nonmem control stream, invisibly. A list with elements 'DATA' and 'INPUT'.
Other Nonmem:
NMapplyFilters()
,
NMextractText()
,
NMreadSection()
,
NMreplaceDataFile()
,
NMwriteSection()
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