data.table := an improved data.frame

I started using a package called data.table just yesterday. I re-wrote the whole of the MayaCalc package to use data.table instead of data.frame. Got it working in a few hours. Syntax is clearer and very concise. As a bonus everything should execute much faster (x10 to x30). I will time MayaCalc today after checking that the results are o.k.
Documentation for data.table is a bit terse, I will write some examples here in a few days’ time.

Be aware though that the semantics is really different when used as an argument to a function. If you use the := operator you achieve the equivalent of passing the data.table argument by REFERENCE rather than the normal R convention of passing all arguments by COPY. This is much faster for large data tables as copying is avoided, but you should be careful even if you understand the difference between these two semantics. If you don’t, do not use data.table before you fully understand the difference and all its implications.

photobiology R packages updated

This is two announce that except for photobiologyVIS and photobiologyUV all packages in the suite have been updated. I tried to make all updates backwards compatible. There are also some new packages on which I have been working for some time that I am publicly releasing today. Vignettes have also been improved.

All packages, even those not updated, have been built now under Windows 7 x64, and are compatible also with x386 (32 bit) versions of Windows.

Continue reading

Thinking, Fast and Slow

Daniel Kahneman (2012) Thinking, Fast and Slow. Penguin Books, London.ISBN 978-0-141-03357-0.

I am currently reading this book. I am finding it extremely interesting. Understanding how and why we make choices, is important for everybody. If you are a scientist or aspire to be one in the future, understanding why we accept more readily some experimental results than others, why we are more comfortable with some hypotheses than others, is of fundamental importance, both to guard against bias, and to be able to present our new ideas in a way that will make them more acceptable. Continue reading

Why are plants green?

This is a frequently posed question, that has no unique or simple answer. Prof. Lars Olof Björn has written a section on this in his book Photobiology: the science of life and light which is much more detailed than this short post. The problem with this question is that its meaning can be different to different persons. I will start by separating different aspects of this question into separate, and better-defined, questions that are easier to answer: Continue reading

photobiology R packages updated

Three packages have had updates:

photobiology (Version 0.2.11)

Mainly speed optimizations, but a couple of functions acquired additional parameters and functionality. All changes are backward compatible.

photobiologyVis (Version 0.1.3)

Modified the wabeband definitions to allow caching of multipliers. No changes to results but a significant speed increase for repeated computations.

photobiologyUV (Version 0.2.4)

Very small changes for consistency of interface. Now all waveband definition functions have a std parameter (even those with only one possible value for it, and have a default value). Changes are backwards compatible.

As usual packages can be downloaded from Buitbucket

SenPEP (Pedro Aphalo’s lab) presentation

SenPEP stands for Sensory Photobiology and Ecophysiology of Plants. Our research group has been active for long, it was born in Suonenjoki in the early 1990’s, moved to Joensuu in 1995, again to Jyväskylä in 2001, and finally to Helsinki in 2006.

Our main research interest is the role of information acquisition by plants and the use of this information during acclimation and for the timing of developmental events. As informational signals are in many cases central to achieving fitness they also must have played and continue to play important roles in evolution.

Possible practical applications are vast, because by manipulating informational signals (e.g. light spectrum, or day length) one can control many plant responses: chemical composition (taste, colour, nutritional value), branching and plant form, timing of flowering, tolerance to physical stress, defenses against pests and diseases, shelf life, etc. Conversely, once the mechanisms of perception and response are understood, it will become easier to manipulate, through breeding, plant responses to informational signals. Continue reading

How to Write a Great Research Paper

Abstract

Professor Simon Peyton Jones, Microsoft Research, gives a guest lecture at the University of Cambridge on writing. Seven simple suggestions: don’t wait – write, identify your key idea, tell a story, nail your contributions, put related work at the end, put your readers first, listen to your readers.

http://www.youtube.com/watch?v=g3dkRsTqdDA

via How to Write a Great Research Paper – YouTube.

photobioloy R packages updated

I have updated all the photobiology packages. There are no major changes, so shouldn’t affect results of calculations or old scripts, except that there was an error in the definition of Green in photobiologyVis (reported by Titta, thanks!).

The documentation is hopefully improved: most packages have now User Guides

As earlier they can be downloaded from Bitbucket as binary (.zip for Windows) or source (.tar.gz). I could also create binaries for Linux if needed, just let me know.