xpose_data: Import NONMEM output into R

In guiastrennec/ggxpose: Diagnostics for Pharmacometric Models

Import NONMEM output into R

Description

Gather model outputs into a R database

Usage

xpose_data(
  runno = NULL,
  prefix = "run",
  ext = ".lst",
  file = NULL,
  dir = NULL,
  gg_theme = theme_readable,
  xp_theme = theme_xp_default(),
  simtab = NULL,
  manual_import = NULL,
  ignore = NULL,
  check_ext = TRUE,
  extra_files,
  quiet,
  ...
)

Arguments

runno	Run number to be used to generate model file name. Used in combination with prefix and ext.
prefix	Prefix to be used to generate model file name. Used in combination with runno and ext.
ext	Extension to be used to generate model file name. Should be one of '.lst' (default), '.out', '.res', '.mod' or '.ctl' for NONMEM.
file	Model file name (preferably a '.lst' file) containing the file extension. Alternative to prefix, runno and ext arguments.
dir	Location of the model files.
gg_theme	A complete ggplot2 theme object (e.g. theme_classic), or a function returning a complete ggplot2 theme.
xp_theme	A complete xpose theme object (e.g. theme_xp_default).
simtab	If TRUE only reads in simulation tables, if FALSE only reads estimation tables. Default NULL reads all tables. Option not compatible with manual_import.
manual_import	If NULL (default) the names of the output tables to import will be obtained from the model file. To manually import files as in previous versions of xpose, the check the function manual_nm_import.
ignore	Character vector be used to ignore the import/generation of: 'data', 'files', 'summary' or any combination of the three.
check_ext	Logical, if TRUE will provide an error message if the extension of the NONMEM input file is not one of '.lst', '.out', '.res', '.mod' or '.ctl' for NONMEM. If FALSE any file extension can be used.
extra_files	A vector of additional output file extensions to be imported. Default is '.ext', '.cov', '.cor', '.phi', '.grd' for NONMEM.
quiet	Logical, if FALSE messages are printed to the console.
...	Additional arguments to be passed to the read_nm_tables functions.

File path generation

The rules for model file names generation are as follow:

• with runno: the full path is generated as <dir>/<prefix><runno>.<ext> e.g. with dir = 'model/pk', prefix = 'run', runno = '001', ext = '.lst' the resulting path would be model/pk/run001.lst

• with file: the full path is generated as <dir>/<file> e.g. with dir = 'model/pk', file = 'run001.lst' the resulting path would also be model/pk/run001.lst. Note: in this case the file extension should be provided as part of the 'file' argument.

Table format requirement

When importing data, an ID column must be present in at least one table for each problem and for each 'firstonly' category. ID columns are required to properly combine/merge tables and removing NA records. If ID columns are missing xpose will return the following warning: Dropped `<tablenames>` due to missing required `ID` column.

Examples

## Not run: 
# Using the `file` argument to point to the model file:
xpdb <- xpose_data(file = 'run001.lst', dir = 'models')

# Using the `runno` argument to point to the model file:
xpdb <- xpose_data(runno = '001', ext = '.lst', dir = 'models')

# Using the `extra_files` argument to import specific output files only:
xpdb <- xpose_data(file = 'run001.lst', dir = 'models', extra_files = c('.ext', '.phi'))

# Using `ignore` to disable import of tables and output files:
xpdb <- xpose_data(file = 'run001.lst', dir = 'models', ignore = c('data', 'files'))

# Using `simtab` to disable import of simulation tables
xpdb <- xpose_data(file = 'run001.lst', dir = 'models', simtab = FALSE)


## End(Not run)

guiastrennec/ggxpose documentation built on June 8, 2024, 3:22 p.m.