79 lines
4.8 KiB
Markdown
79 lines
4.8 KiB
Markdown
---
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author: einar
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comments: true
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date: 2009-02-07 18:55:53+00:00
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layout: post
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slug: science-and-kde-rkward
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title: 'Science and KDE: rkward '
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wordpress_id: 533
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categories:
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- KDE
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- Linux
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- Science
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tags:
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- KDE
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- Linux
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- R
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- rkward
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- Science
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---
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I try to use FOSS extensively for my scientific work. In fact, when possible, I use _only_ FOSS tools. Among these there is the R programming language. It's a Free implementation of the S-plus language, and it's mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don't like R much. But sometimes it's the only alternative.
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Well, what does R have to do with KDE? With this post I'd like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I'll focus on rkward, a GUI front-end for R.
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**Introduction**
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Although R is a programming language, it's mainly used in an interactive session, started from the terminal. The standard installation can be improved by the use of add-on packages, _libraries_ in R-speak, which can be installed from the Internet (Comprehensive R Archive Network or CRAN) or from local files. One of the most famous third party repositories is the Bioconductor project, which hosts a lot of packages used by life scientists who do bioinformatics.
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The Windows version of R has a GUI (Rgui) which provides extra functionality, such as package management and loading, and other goodies. Although there were plan for a GTK+ frontend for Linux, the project is (as far as I know) stuck in a limbo.
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That's where rkward comes to the rescue. It's a GUI front-end for R for KDE4, which aims to provide a graphical shell for many R commands and environments (and especially the publication-quality plotting figures).
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**Getting rkward**
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rkward is available from [Sourceforge.net](http://rkward.sourceforge.net/). Unfortunately, if you use a recent (>=2.8) version of R it won't compile, due to the changes in R itself. For that, you need to directly download the sources off SVN with a command like this
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{% highlight cpp %}
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svn co https://rkward.svn.sourceforge.net/viewvc/rkward/trunk/rkward/
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{% endhighlight %}
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Either way, the sources are compiled the usual, way, that is
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{% highlight cpp %}
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cd rkward-xxx # Your rkward source dir
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mkdir build; cd build
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cmake -DCMAKE_INSTALL_PREFIX=`kde4-config --prefix` ../
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make
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{% endhighlight %}
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Followed by `make install` as root or using sudo, depending on your distribution.
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**rkward at a glance**
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**[singlepic id=263 w=320 h=240 float=center]**
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This is how rkward looks when loading it up (yes, it's in Italian because that is my own locale). You have the R console (which I brought up) and then an output window which is used to display results. There is also another tab called "mio.dataset" (my.dataset) which keeps data, in a spreadsheet-like form. This is useful when you want to create your own datasets from scratch, or if you want to inspect one you have loaded.
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So how do you start coding? You can create a new script using the "Script File" button. Like that, you can input R commands and then execute them all at once, or the current line. If you prefer interactive work, you can use the R command line (shown in the screenshot).
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[singlepic id=264 w=320 h=240 float=center]
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You can also use rkward to import data: R provides a series of functions (like `read.table`) to load data sets (usually comma- or tab-delimited text files). rkward provides a complete GUI to those functions, which is shown in the screenshot above. Notice that for working, it requires PHP (the line command version).
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[singlepic id=266 w=320 h=240 float=center]
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Ok, we have data loaded. Now we may want to do some operations: rkward provides front-ends to many of R's statistical functions. In the screenshot, we can see the GUI for a two-variable t-test. Notice how it shows also the code, so the most experienced R people can view exactly what it does.
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Like with statistics, R has powerful support for graphics, and even in this case rkward offers some frontends, for example histograms, boxplots, and scatter plots. You can also plot all kinds of distributions.
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[singlepic id=265 w=320 h=240 float=center]
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Lastly, rkward can manage your R packages (R package management is akin to one of a Linux distribution), and als your package sources. You can install or upgrade packages, and select where they'll get installed to.
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**Conclusions**
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rkward is a nice frontend for the R programming language, which adds a GUI with the power of KDE to R. Unfortunately the program is still somewhat unstable (also shown by a warning when you run it) and its main developer has currently very little time to work on it. In case you may want to help, you can hop to the r[kward-devel mailing list.](http://sourceforge.net/mailarchive/forum.php?forum_name=rkward-devel)
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