Reading NONMEM table files

Reads one or more NONMEM table files, removes duplicated columns and merges the data into a data.frame.

Usage

read.nm.tables(
  table.files = NULL,
  runno = NULL,
  tab.suffix = "",
  table.names = c("sdtab", "mutab", "patab", "catab", "cotab", "mytab", "extra", "xptab"),
  cwres.name = c("cwtab"),
  cwres.suffix = "",
  quiet = FALSE,
  new_methods = TRUE,
  ...
)

Arguments

table.files

Exact names of table files to read. If not provided then the exact names are created using the other arguments to the function.

runno

Run-number to identify sets of table files.

tab.suffix

Table file name suffix.

table.names

Vector of template table file names to read.

cwres.name

Vector of CWRES table file names to read.

cwres.suffix

CWRES table file name suffix.

quiet

Logical value to indicate whether some warnings should be quiet or not.

new_methods

Should faster methods of reading tables be used (uses readr package)?

...

Additional arguments passed to this function

Value

A dataframe.

Details

Reads one or more table files, removes duplicate columns and merges the data. The function also checks to see if the table files are of the same length (required).

If there are header lines in the table files (for example if your data are simulated with NSUB>1), these are removed.

The table file names to read are constructed from the file name templates of table.names. The runno and tab.suffix are appended to the file name template before checking if the file is readable.

Xpose expects, by default, to find the following NONMEM tables in the working directory to be able to create an Xpose data object (using a run number of 5 as an example):

sdtab5: The 'standard' parameters, including IWRE, IPRE, TIME, and the NONMEM default items (DV, PRED, RES and WRES) that are added when NOAPPEND is not present in the $TABLE record.

$TABLE ID TIME IPRE IWRE NOPRINT ONEHEADER FILE=sdtab5

patab5: The empirical Bayes estimates of individual model parameter values, or posthoc estimates. These are model parameters, such as CL, V2, ETA1, etc.

$TABLE ID CL V2 KA K F1 ETA1 ETA2 ETA3 NOPRINT NOAPPEND ONEHEADER FILE=patab5

catab5: Categorical covariates, e.g. SEX, RACE.

$TABLE ID SEX HIV GRP NOPRINT NOAPPEND ONEHEADER FILE=catab5

cotab5: Continuous covariates, e.g. WT, AGE.

$TABLE ID WT AGE BSA HT GGT HB NOPRINT NOAPPEND ONEHEADER FILE=cotab5

mutab5, mytab5, extra5, xptab5: Additional variables of any kind. These might be useful if there are more covariates than can be accommodated in the covariates tables, for example, or if you have other variables that should be added, e.g. CMAX, AUC.

See also

xpose.data-class, compute.cwres

Other data functions: add_transformed_columns, change_graphical_parameters, change_misc_parameters, compute.cwres(), data.checkout(), data_extract_or_assign, db.names(), export.graph.par(), export.variable.definitions(), import.graph.par(), import.variable.definitions(), make.sb.data(), nsim(), par_cov_summary, read.TTE.sim.data(), read_NM_output, read_nm_table(), simprazExample(), tabulate.parameters(), xlabel(), xpose.data, xpose.print(), xpose4-package, xsubset()

Author

Niclas Jonsson, Andrew Hooker

Examples

if (FALSE) {
## We expect to find the required NONMEM run and table files for run
## 5 in the current working directory, and that the table files have
## a suffix of '.dat', e.g. sdtab5.dat

my.dataframe <- read.nm.tables(5, tab.suffix = ".dat") 
}