2 Installation

IQR Tools has been developed as a software package for the well-established and free statistical software environment R.

2.1 Requirements

  • Supported R Versions: 3.4.1 -> latest R version cited on the Microsoft R Application Network
  • Supported operating systems: Windows (32 and 64 bit), Linux, Mac

2.2 Rtools on Windows

For the compilation of models a C-compiler is needed on Windows. The easiest way to ensure that is to install “Rtools”, which can be found here: https://cran.r-project.org/bin/windows/Rtools/. Currently version 3.4 or 3.5 is a good choice.

As Rtools can be cumbersome to install, a convenient installer has been made available that does not require administrator rights. Execute the following in R:

source("https://iqrtools.intiquan.com/install.R")
install_Rtools()

If you have a prior installation of Rtools it will not be overwritten. If you want to use the installer you will need to delete the folder “C:\Rtools” before running the installer.

2.3 IQR Tools

A convenient installation function has been provided for IQR Tools that allows to install a defined version of the package and also takes care of all dependencies.

2.3.1 Newest Version

Installation of the always newest available version of IQR Tools can be done by running the following commands:

source("https://iqrtools.intiquan.com/install.R")
installVersion.IQRtools() 

If dependencies are missing then the user is notified and needs to install them manually. The installer also provides the means to install all dependencies, which is done using the optional argument forceDependencies in the following manner:

source("https://iqrtools.intiquan.com/install.R")
installVersion.IQRtools(forceDependencies=TRUE) 

When forcing all the dependencies, these are installed from the MRAN time machine repository that matches the R version, which is good to ensure reproducibility of results. Read more on reproducibility here.

2.3.2 Redhat 6 / Centos 6

On Redhat 6 and Centos 6 operating systems an additional argument needs to be provided. On these systems, IQR Tools can be installed as follows:

source("https://iqrtools.intiquan.com/install.R")
installVersion.IQRtools(centosRedhat6=TRUE) 
# Or by 
installVersion.IQRtools(forceDependencies=TRUE,centosRedhat6=TRUE) 

2.3.3 Defined Version

Software evolves, and so do R packages. Using CRAN on a daily basis has become a < a href=“reproducibility.html#CRANnighmare”>reproducibility nightmare. To allow users to rerun analyses that have been conducted with a specific version of IQR Tools, the installer allows to define the version to be installed. The following example will install version “0.9.1”. Replace the version number by your desired version. The other optional input arguments to the function still can be used as needed (forceDependencies and centosRedhat6).

source("https://iqrtools.intiquan.com/install.R")
installVersion.IQRtools("0.9.1") 

2.4 Setup after installation

After the above installation, please locate the folder in which IQR Tools has been installed. In this folder there is a file called setup_options_IQRtools.R. Please have a look in this file and edit it as appropriate. It realizes the interfaces to NONMEM and MONOLIX and has other customization possibilites that might be needed on your system. You also can call the function setup_IQRtools() which will open the setup file in an editor and allow editing.

In case you do not have admin rights and the IQR Tools installation is a global one, then you can call setup_IQRtools(local=TRUE), which allows you to overwrite the global settings locally (if allowed by your system administrator).

2.5 Activation

The newest version of IQR Tools, as installed above, comes as a fully functional version, right out of the box. After a certain period IQR Tools will ask for an activation key. In this case, please either contact info@intiquan.com or just install the then newest version.

2.6 IQReport

IQReport is the IntiQuan Word report generator that allows to efficiently write full reports in an extended Markdown syntax. Resulting reports are fully submission ready and the used Word style is customizable to match a specific organisational requirement.

R plots and data.frames can easily be incorporated into such Word documents without the need for manual copy paste approaches. As functions in IQR Tools do generate a larger number of tables and plots, the required output format already matches the requirement of IQReport.

IQReport can be otbained from here: https://iqreport.intiquan.com. If the default installation location is chosen, no changes in the IQR Tools setup need to be done. If a different installation location is chosen, update the relevant IQReport information by editing the setup_options_IQRtools.R file, as described in Section 2.4. If the following installer is used, no updates to the setup file need to be done and installation is directly from R:

source("https://iqrtools.intiquan.com/install.R")
install_IQReport()

2.7 IQRsbml

Especially in the area of Systems Pharmacology modeling it might be of interest to a user to be able to import models in the Systems Biology Markup Language (SBML) to R. SBML in general is very badly supported on R and the available SBML packages should not be trusted to be able to handle a reasonble fraction of SBML models.

To counteract this lack of SBML import in R, the IQRsbml software has been made available as a stand-alone executable. For good reasons it is only available for Windows machines. Once installed, the setup_options_IQRtools.R file might need to be updated, as described in Section 2.4. If the following installer is used, no updates to the setup file need to be done and installation is directly from R:

source("https://iqrtools.intiquan.com/install.R")
install_IQRsbml()