nm_tables: Read all tables and input data

In metrumresearchgroup/bbr: R package for bbi

Read all tables and input data

Description

Reads in the input data set and all table output files from a NONMEM run. This function will return a named list with all the relevant tibbles. To return a single tibble with the input data joined to the relevant table outputs, use the related nm_join() function. This function will print the number of rows and columns when each file is loaded. This printing can be suppressed by setting options(bbr.verbose = FALSE).

Usage

nm_tables(
  .mod,
  .files = nm_table_files(.mod),
  read_multi_tab = TRUE,
  table_pattern = "TABLE NO",
  ...
)

nm_table_files(.mod, .check_exists = TRUE)

Arguments

.mod	A bbi_nonmem_model or bbi_nonmem_summary object, or a path to a NONMEM run.
.files	Character vector of file paths to table files to read in. Defaults to calling nm_table_files() on .mod, which will parse all file names from ⁠$TABLE⁠ blocks in the control stream. If passing manually, paths should be either absolute, or relative to get_output_dir(.mod).
read_multi_tab	Logical (T/F). If TRUE, read in files with multiple tables per file. Otherwise they will be skipped.
table_pattern	character string (fixed) defining the start of a new table. Only used if read_multi_tab = TRUE (passed to nm_file_multi_tab()).
...	additional arguments passed to nm_file_multi_tab().
.check_exists	If TRUE check if files exist.

Details

As described in Value, nm_tables() returns a named list of tibble(s). To return a single tibble will all of this data joined together, see nm_join().

Value

A named list of tibbles. The first element will always be named data and will contain the input data set. Subsequent elements will be named for the file from which they were loaded, with get_model_id(.mod) (and .) removed from the beginning and end, if present. For example, a model named ⁠001.ctl⁠ that generated a table named ⁠001.tab⁠ will have the relevant element named tab. Column names in all tibbles will be converted to uppercase.

Functions

• nm_table_files(): Extract paths to table output files from NONMEM control stream, and optionally check if the files exist.

See Also

nm_join(), nm_file(), nm_file_multi_tab()

metrumresearchgroup/bbr documentation built on March 29, 2025, 1:08 p.m.