Before I forget: a few links about starting up in Python for scientific projects:
Now if we had a great Python library for linear mixed models life would be easier.
It has been month and a half since I compiled a list of statistical/programming internet flotsam and jetsam.
- Via Lambda The Ultimate: Evaluating the Design of the R Language: Objects and Functions For Data Analysis (PDF). A very detailed evaluation of the design and performance of R. HT: Christophe Lalanne. If you are in statistical genetics and Twitter Christophe is the man to follow.
- Attributed to John Tukey, “without assumptions there can be no conclusions” is an extremely important point, which comes to mind when listening to the fascinating interview to Richard Burkhauser on the changes of income for the middle class in USA. Changes to the definition of the unit of analysis may give a completely different result. By the way, does someone have a first-hand reference to Tukey’s quote?
- Nature news publishes RNA studies under fire: High-profile results challenged over statistical analysis of sequence data. I expect to see happening more often once researchers get used to upload the data and code for their papers.
- Bob O’Hara writes on Why simple models are better, which is not positive towards the machine learning crowd.
- A Matlab Programmer’s Take On Julia, and a Python developer interacts with Julia developers. Not everything is smooth. HT: Mike Croucher.
- Dear NASA: No More Rainbow Color Scales, Please. HT: Mike Dickinson. Important: this applies to R graphs too.
- Rafael Maia asks “are programmers trying on purpose to come up with names for their languages that make it hard to google for info?” These are the suggestions if one searches Google for Julia:
Unhelpful search suggestions.
- I suggest creating a language called Bieber and search for dimension Bieber, loop Bieber and regression Bieber.
That’s all folks.
It has been a strange last ten days since we unexpectedly entered grant writing mode. I was looking forward to work on this issue near the end of the year but a likely change on funding agency priorities requires applying in a few weeks; unfortunately, it means that all this is happening at the same time I am teaching.
And that’s all folks.
This coming Monday we start the first semester in Canterbury (and in New Zealand for that matter). We are all looking forward to an earthquake-free year; more realistically, I’d be happy with low magnitude aftershocks.
- The Wall Street Journal reports that more pediatricians are ‘firing’ patients that refuse to use vaccines. I’m wondering about practices that will cluster with ‘vaccine refusers’.
- I am collaborating with a researcher in Electrical Engineering where he and his students develop very cool tools for us (see example in this previous post on dealing with autocorrelation in mixed models). They use Python to control the tools, data extraction and do some basic processing (isn’t that cool?). Python + Scipy have moved a lot towards creating a nice environment for scientific computing; however, in my opinion setting an R environment is way easier than dealing with all the versions for python, wxpython, etc. At the end I went for the 32 bit version in OS X because 64 bit is not supported (wxpython targets carbon, meh).
- Why not publish your data too? HT: @chlalanne. I’ll be uploading datasets that I’ve used in my papers (at least the ones that do not contain industry/confidential data).
- Timandra Harkness asks Have you been seduced by statistics? in Significance Journal (free access). In the same issue Matt Briggs asks another important question Why do statisticians answer silly questions that no one ever asks?
- How companies learn your secrets: the creepy side of statistics/machine learning.
- Feeling all smug in a discussion in Engineering: people struggling with software licensing (Office, Matlab, etc). I pointed out that we didn’t have any licensing issues with R to be at the bleeding edge when teaching. Take that!
- In the nothing-to-do with-stats category, Retronaut displays a beautiful collection of Soviet space propaganda posters. HT: can’t remember.
Supermarkets in New Zealand, Are they creepy too? Checkouts at Pak N Save, Christchurch (Photo: Luis).
I’ve been running analyses for two to three papers, mostly using R + asreml-R + ggplot2 + plyr. I hope to write one of them using XeLaTeX (I’ll be the sole author), while in the other(s) I am condemned to MS Word (!). Thinking of journals to send the papers to, with the most liberal copyright as possible (hard in forestry).
P.S. Flotsam posts compile small bits of information, twitter favorites, shared links, etc.
I installed the latest version (0.12) of IPython from source in my mac, but forgot that I had a previous version (0.10) installed using easy_install. When trying to run ipython I kept getting the error:
No module named terminal.ipapp.
Fixing it. I ran
easy_install -m ipython in Terminal, so Python doesn’t continue looking for the old package, as explained here. Then I was able to navigate to /Library/Python/2.6/site-packages and then use
rm -r ipython-0.10.1-py2.6.egg. Now everything works fine.