Read an output table file from Nonmem

Read a table generated by a $TABLE statement in Nonmem. Generally, these files cannot be read by read.table or similar because formatting depends on options in the $TABLE statement, and because Nonmem sometimes includes extra lines in the output that have to be filtered out. NMreadTab can do this automatically based on the table file alone.

NMreadTab(
  file,
  col.tableno,
  col.nmrep,
  col.table.name,
  header = TRUE,
  skip,
  quiet = TRUE,
  as.fun,
  ...
)

Arguments

file

path to Nonmem table file

col.tableno

In case of simulations where tables are being repeated, a counter of the repetition number can be useful to include in the output. For now, this will only work if the NOHEADER option is not used. This is because NMreadTab searches for the "TABLE NO..." strings in Nonmem output tables. If col.tableno is TRUE (default), a counter of tables is included as a column called NMREP. Notice, the table numbers in NMREP are cumulatively counting the number of tables reported in the file. NMREP is not the actual table number as given by Nonmem.

col.nmrep

col.nmrep If tables are repeated, include a counter? It does not relate to the order of the $TABLE statements but to cases where a $TABLE statement is run repeatedly. E.g., in combination with the SUBPROBLEMS feature in Nonmem, it is useful to keep track of the table (repetition) number. If col.nmrep is TRUE, this will be carried forward and added as a column called NMREP. This is default behavior when more than one $TABLE repetition is found in data. Set it to a different string to request the column with a different name. The argument is passed to NMscanTables.

col.table.name

The name of a column containing the name or description of the table (generated by Nonmem). The default is "table.name". Use FALSE not to include this column.

header

Use header=FALSE if table was created with NOHEADER option in $TABLE.

skip

The number of rows to skip. The default is skip=1 if header==TRUE and skip=0 if header==FALSE.

quiet

logical stating whether or not information is printed about what is being done. Default can be configured using NMdataConf.

as.fun

The default is to return data as a data.frame. Pass a function (say tibble::as_tibble) in as.fun to convert to something else. If data.tables are wanted, use as.fun="data.table". The default can be configured using NMdataConf.

...

Arguments passed to fread.

Value

The Nonmem table data.

Details

The actual reading of data is based on data.table::fread. Generally, the function is fast thanks to data.table.

See also

Other DataRead: NMreadCsv(), NMscanData(), NMscanInput(), NMscanTables()