R-tools

What is it

R-Tools is a MediaWiki extension that allows registered Opasnet users to run R code directly from a wiki page.

Libraries

Opasnet R software has some additional libraries installed for plotting (e.g. ggplot2) and also some libraries that enable connecting to external databases (e.g. OpasnetBaseUtils). More libraries can be installed on request with proper reasons.

Usage

R-tools uses <rcode> tags. Any R code written between these tags can be run from wiki page using the "Run code"-button. Press the button and new window (or tab) opens up showing the status and the results of the run in real time. An example code that counts one plus one using R:

<rcode>
1+1
</rcode>

Parameters

Some optional parameters can be given to <rcode> tag as described below.

• graphics - If the code is meant to draw any graphs then define graphics to '1'.
• variables - Allows user to input values for named variables in R code. Inputs will be displayed in a box below the actual R code in wiki page. Variables syntax is described in its own chapter in this page.

Variables syntax

Each variable needs three attributes separated with | (pipe) character. These attributes (in correct order) are variable name in code,variable description in wiki page and default value. Variable triplets must also be separated with pipe. An example R code with two defined attributes calculates the area of a rectangle:

<rcode variables="width|Width of the rect|10|height|Height of the rect|10">
# The area of the rect is
width *  height
</rcode>

Note that variable default value can also be a string or even an array (e.g. c(1,2,3) or 'Some name').