Sunday, March 28, 2010

Eclipse setup notes: R (StatEt) and Python (Sage)

My standard Eclipse setup consists of the following extensions:
  • Texclipse
  • StatEt (for R and Sweave)
  • Pydev
  • Data Tools
  • BIRT
And I also have these loaded, even if I don't use them as much
  • CDT (C/C++ Developers tools)
  • Java (since it comes with)
  • Subversion
For a while I've been using StatEt using the R console, because I had not gotten the RJava console to work. While it works, it has two problems (1) it does not open a graphics display, so you could not see the plots you were making (But plots are still generated and included into Sweave documents) and (2) it would drop out if there were any errors in the R code, causing you to have to start over.

The trick with getting RJava to work is set the configuration in the JRE tab in eclipse. In the VM Arguments, there should be an option included that points to rJava (which you have installed and run
sudo R CMD javareconf
to enable)


(where the / is your path to the location you installed your rJava library in the R directory. On my system it is /home/my_account/R/i486-pc-linux-gnu-library/2.9/ )

This provides a stable interactive R console and allows Sweave.

For Python, in addition to the standard interpreters (python, jython, ipy), you can run Sage. This would be through using the Python interpreter that is in the Sage package.

So add another Python interprester pointing to /sage-4.x.x/bin/python
With $SAGE_ROOT = /path/to/sage-4.x.x
and LD_LIBRARY_PATH = $SAGE_ROOT/local/lib

Next steps, figure out how to add R libraries to the R included in Sage, so R packages can be called from within Sage (note that R can be called using the rpy2 package, but this is only the currently installed packages.)

Wednesday, March 24, 2010

PSO: A conversation with strings that are different

[Originally posted at the Pittsburgh Symphony Orchestra: Outside Perspectives]

Having a viola as soloist was a change from the usual piano or violin guest artist. I was laughing reading the program notes saying that Berlioz Harold in Italy was written for Paganini, who complained that it did not allow him to play enough. Because Berlioz wrote a different kind of piece.

While it may not have satisfied a violin virtuoso, what Berlioz gave us was a conversation. Instead of the violin soaring exuberantly, we were treated to viola, harp, and flutes passing their lines to one another. Each different, yet fitting together like old friends engaged in conversation.

My wife and I have not been married long, but we sometimes get to enjoy the moments where we can talk about subjects ending with the wonder "you think about that too!?", the times when we can finish each other's thoughts (which is real useful when one has trouble coming up with the next word), and "magic" around the house. But, in our unsentimental times, we have some understanding of how the "magic" happens, it is the paying attention to each other and around us, and it almost seems natural. So it is with the first movements of Harold. The principals are not the type to overwhelm with brilliance, instead we hear them play with each other, bow, pluck and wind. Appreciative both of the differences and their ability to be together. And hoping life will be like that as well.

Sunday, March 07, 2010

Is it [being married] all that you expected?

Somehow, we (the married for ~20 months couple) got asked if "being married was all we expected?" We did not really answer the question. And I'm not sure we had expectations all things considered. Marriage was more something we got into thinking we could make work more then something we had dreams and aspirations for. Of course, a relationship seemed the same, it was something that could work, more then something of dreams.

There are lots of examples of things to be afraid of. We both know people whose lives lost much in richness, became uninteresting, and definition when they became involved in romantic relationships, and replaced what we knew with a life completely defined only by their relationship, viewing the world only through the lens of romantic relationships, and viewing those who did not share this with disdain. I know of others who viewed their romantic relationships as prizes and possesions, that they would rather have the partner dead then with others, with all the righteousness of their God to justify them. And we have known people who were the possession or prize.

Did this happen with us? Some old interests faded away. Although living it, it feels like this is the natural progressions of interests, in the course of events our interests change, some fade away, others are added, and hopefully some get deeper. But having someone else there changes the direction. It is not that we share all the same interests (or that is ever going to happen, as anyone who knows us will no doubt affirm), but others are shared, and sharpened. Because there is little that sharpens more then someone else who can challenge, affirm, question, and support in ones endeavours and goals.

But this was not something that would lead to marriage. In the end the question was about living life. To take in the joys and the challenges, life's uncertainties and the rewards that may or may not be there. To recognise there are no guarantees in life, not even what is in life right now.

When we were dating, someone told me that the time we were apart when I was deployed overseas did not count when considering the time in relationship. I disagree. One of the results is that our relationship was stressed. It would not be the first such stress. My wife has joked that she thinks she found herself in a movie plot. And no doubt there will be more stresses and changes to come. And we will both change along the way as these stresses come, so it was good to learn how this happens. And probably even more important to learn how we undergo change then what the changes actually were. Neither of us is the same as the person we were when we met, when we got engaged, or when we got married. And it is better that way.