EL009: Missing Values in Clinical Research

This website contains materials for the NIHES course Missing Values in Clinical Research (EL009):

• lecture slides
• practicals

Download a .zip file with all materials:

The practicals require R, and JAGS (necessary for the parts of the practical that use the JointAI package) needs to be installed.

To download and install R, go to https://cran.r-project.org/.

To download JAGS, go to https://sourceforge.net/projects/mcmc-jags/files/.

Software

The practicals require R, and JAGS (necessary for the parts of the practical that use the JointAI package) needs to be installed.

R

You can download R here:

• Windows: https://cran.r-project.org/bin/windows/base/
• Mac OS: https://cran.r-project.org/bin/macosx/
• Linux: https://cran.r-project.org/bin/linux/

It is strongly recommended to use a recent version of R, i.e., version 4.3.0

To check the version number of R, you can use the following syntax (in R):

R.version.string

JAGS

To download the latest version of JAGS, go to https://sourceforge.net/projects/mcmc-jags/files/.

The JAGS version should be 4.3.0 or later.

R packages

You will also need the following R packages:

install.packages("mice")
install.packages("JointAI")
install.packages("ggplot2")
install.packages("corrplot")

For the packages mice and JointAI it is important that you have recent versions installed.

• mice version 3.15.0 or later
• JointAI version 1.0.5

To check which version of a package you have installed, you can use the function packageVersion(), for example

packageVersion("JointAI")
packageVersion("mice")

Once you have the package JointAI installed¹, you can use the following syntax to check if R can find JAGS, and which version of JAGS is installed:

rjags::jags.version()

There are a number of additional packages that may be useful:

install.packages("VIM")
install.packages("naniar")
install.packages("visdat")