ubiquity (version 2.1.0)

system_fetch_template: Create New Analysis Template

Description

Building a system file will produce templates for R and other languages. This function provides a method to make local copies of these templates.

Usage

system_fetch_template(
  cfg,
  template = "Simulation",
  overwrite = FALSE,
  output_directory = getwd()
)

Value

List with vectors of template sources, destinations

and corresponding write success (write_file), also a list element indicating the overall success of the function call (isgood)

Arguments

cfg

ubiquity system object

template

template type

overwrite

if TRUE the new system file will overwrite any existing files present

output_directory

directory where workshop files will be placed (getwd())

Details

The template argument can have the following values for the R workflow:

• "Simulation" produces analysis_simulate.R: R-Script named with placeholders used to run simulations

• "Estimation" produces analysis_estimate.R: R-Script named with placeholders used to perform naive-pooled parameter estimation

• "NCA" produces analysis_nca.R: R-Script to perform non-compartmental analysis (NCA) and report out the results

• "ShinyApp" produces ubiquity_app.R, server.R and ui.R: files needed to run the model through a Shiny App either locally or on a Shiny Server

• "Model Diagram" produces system.svg: SVG template for producing a model diagram (Goto https://inkscape.org for a free SVG editor)

• "Shiny Rmd Report" produces system_report.Rmd and test_system_report.R: R-Markdown file used to generate report tabs for the Shiny App and a script to test it

And this will create files to use in other software:

• "Adapt" produces system_adapt.for and system_adapt.prm: Fortran and parameter files for the currently selected parameter set in Adapt format.

• "Berkeley Madonna" produces system_berkeley_madonna.txt: text file with the model and the currently selected parameter set in Berkeley Madonna format

• "nlmixr" produces system_nlmixr.R For the currently selected parameter set to define the system in the `nlmixr` format.

• "NONMEM" produces system_nonmem.ctl For the currently selected parameter set as a NONMEM conntrol stream.

• "Monolix" produces system_monolix.txt and system_monolix.mlxtran For the currently selected parameter set.

• "mrgsolve" produces system_mrgsolve.cpp: text file with the model and the currently selected parameter set in mrgsolve format

Examples

# \donttest{
# Creating a system file from the mab_pk example
fr = system_new(file_name        = "system.txt", 
                system_file      = "mab_pk", 
                overwrite        = TRUE, 
                output_directory = tempdir())

# Building the system 
cfg = build_system(system_file  = file.path(tempdir(), "system.txt"),
      output_directory          = file.path(tempdir(), "output"),
      temporary_directory       = tempdir())

# Creating a simulation template
fr =  system_fetch_template(cfg, 
      template         = "Simulation", 
      output_directory = tempdir())
# }