Evolving notes, images and sounds by Luis Apiolaza

Category: python (Page 1 of 3)

Python not suitable platform for reproducible research

While [Active Papers] has achieved its mission of demonstrating that unifying computational reproducibility and provenance tracking is doable and useful, it has also demonstrated that Python is not a suitable platform to build on for reproducible research. Breaking changes at all layers of the software stack are too frequent.

Konrad Hinsen in Archiving Active Papers

I started using Python for my PhD around 1997, to control simulations I wrote using Fortran 90. I chose Python based on Konrad Hinsen’s writings at the time in a long-disappeared website. A few years later I moved all my work to R, which I found much more stable. I have some 20-year-old R base code that still runs. 😇

Incidentally, last year I wrote a series of posts on Some love for base R.

Flotsam 13: early July links

Man flu kept me at home today, so I decided to do something ‘useful’ and go for a linkathon:

Over and out.

Pythonic links

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.

Late-April flotsam

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.

That’s all folks.

Early-March flotsam

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.

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