system_fetch_template: Create New Analysis Template

In john-harrold/ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools

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()
)

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

• "myOrg" produces myOrg.R: R-Script for defining functions used within your organization

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.R For the currently selected parameter set as a NONMEM conntrol stream.

• "Monolix" produces system_monolix.txt For the currently selected parameter set as a NONMEM conntrol stream.

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

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)

Examples

# 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())

john-harrold/ubiquity documentation built on March 13, 2024, 2:58 a.m.