openVA
Check out the package and team website for more details and
documentations: openVA.net
What’s new
Installation instructions
This guide presents an overview for installing
openVA package, with some common error reports and
solutions at the end.
1. Overview of openVA
package structure
Whenever the openVA package is loaded to R, it also
requires four other core packages on CRAN for each of the VA coding
methods, namely, InSilicoVA, InterVA4,
Tariff, and nbc4va, and
ggplot2 for visualization. Additionally, the
InSilicoVA package further requires the dependency of
coda and rJava for its
computation.
Users typically need to take no specific action regarding the
dependencies, since R takes care of them automatically. However,
sometimes issues with installing openVA package can
arise because of some of the dependencies, which may require additional
configurations and re-installing the package. I find that most of the
times, the errors stem from loading rJava, and thus is
the main focus of this guide.
2. Pre-requisites
As the name suggests, to properly load the package
rJava, you will need two key ingredients: R,
and Java. Here is how you can make sure you have the right
combination of the two:
Check R environment
- If you do not already have it, install from CRAN. Follow the instructions at
the link to choose a mirror that will take you to the download page.
After download, double click the file to install.
- Open R. On the welcome message, there is a line starting with
“Platform” and ending with “(32-bit)” or “(64-bit)”. It is very
important to know which version (32-bit or 64-bit) of R you use, since
the Java JDK should have the same version.
- Sometimes multiple versions of R could be installed on the same
machine, so you should check the version you wish to use for data
analysis. For example, if you prefer using RStudio to run the codes, you
should check the default R version of RStudio by reading the welcome
message for RStudio, instead of, say, the R version when opening from
command line.
Check Java installation
- To check if Java in installed on your Mac or
Linux machine, open terminal if you use Mac or Linux
and type in
java -version
. If Java is installed, it will
show the Java version number. Version number at least 1.7.x should be
sufficient.
- To check if Java is installed on your Windows
machine, open Control Panel, select
Programs, then select Programs and
Features, and see if Java is listed.
- If no Java is installed (on Mac OSX, you will see a pop-up notice of
installing Java JDK), or version too low, you should download and
install a newer Java. The required download is JDK (Java Development
Kit). Click on download link for JDK and choose the appropriate version.
You should choose “x86” version if your R version is 32-bit, and “x64”
if R is 64-bit. Then follow the instructions to finish download and
install Java.
- After successfully installing Java, try again typing
java -version
on terminal or Command Prompt. It should show
the correct version number just installed.