build_system: Build the System File

In ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools

Build the System File

Description

Builds the specified system file creating the targets for R and other languages as well as the templates for performing simulations and estimations.

Usage

build_system(
  system_file = "system.txt",
  distribution = "automatic",
  perlcmd = "perl",
  output_directory = file.path(".", "output"),
  temporary_directory = file.path(".", "transient"),
  verbose = TRUE,
  ubiquity_app = FALSE,
  debug = TRUE
)

Arguments

system_file	name of the file defining the system in the ubiquity format (default = 'system.txt'), if the file does not exist a template will be created and compiled.
distribution	indicates weather you are using a 'package' or a 'stand alone' distribution of ubiquity. If set to 'automatic' the build script will first look to see if the ubiquity R package is installed. If it is installed it will use the package. Otherwise, it will assume a "sand alone" distribution.
perlcmd	system command to run perl ("perl")
output_directory	location to store analysis outputs (file.path(".", "output"))
temporary_directory	location to templates and otehr files after building the system (file.path(".", "transient"))
verbose	enable verbose messaging (TRUE)
ubiquity_app	set to TRUE when building the system to be used with the ubiquty App (FALSE)
debug	Boolean variable indicating if debugging information should be displayed (TRUE)

Value

initialized ubiquity system object

Examples

fr = system_new(file_name        = "system.txt", 
                system_file      = "mab_pk", 
                overwrite        = TRUE, 
                output_directory = tempdir())
cfg = build_system(system_file  = file.path(tempdir(), "system.txt"),
      output_directory          = file.path(tempdir(), "output"),
      temporary_directory       = tempdir())

ubiquity documentation built on May 29, 2024, 12:02 p.m.