Aims and features

I had two conflicting aims when designing this suite of packages: easy of use and good performance. It has not been always possible to achieve both with the same code. Because of this, the defaults tend to favour easy of use and precision. However, the alternative functions or arguments allow the tuning for performance at the expense of easy of use. I aimed at having an easy to use command-line user-interface, because I wanted to develop packages that could be used both for teaching photobiology and for real data analysis, including scripting. Performance is important in our own research as we have close to a million daylight spectra to analyse in detail, starting from raw spectrometer detector counts.

While writing the packages I learnt a lot about programming R and some of the internals of packages like data.table and ggplot2. Because of this I rewrote quite a lot of the code at least twice. Many people, knowingly or not have been helping with this project. From companies allowing the use of data sets, developers of R itself and other packages, and all those who answered to my own and other people’s questions in Stackoverflow and other web forums. Of course everybody in my research group had some influence.

In parallel with the writing of the code I have been writing a Handbook to accompany it, with Andreas Albert as co-author and other people contributing ideas and feedback. Simply using the packages in the handbook and trying to explain how to use them, made me re-think many of the details of the user-interface, I think that the basic interface is almost settled by now, but there is still much to do. In particular, although many of the code examples in the new Handbook are written, the explanatory text and the explanations about the math behind the calculations are still mostly missing.

New updates

photobiology 0.3.10 : A major update. New functionality, specially related to plotting, and after lots of testing quite many bugs squashed.

photobiologygg 0.1.10 : A very minor update for compatibility with photobiology 0.3.10

photobiologyWavebands 0.1.0 : A new package, a merge of photobiologyUV and photobiologyVIS plus some new additions.

photobiologyUV 0.3.0 : Now a dummy package for backwards compatibility. Deprecated.

photobiologyVIS 0.2.0 : Now a dummy package for backwards compatibility. Deprecated.

photobiologyAll 0.1.1 : Changed so that it now loads photobiologyWavebands

Note 1: These packages updates are interdependent, if you update you will need to update them all. If you update from the repository this will happen automatically.

Note 2: I have uploaded source packages (for all OSs and R 3.x.x) and Windows binaries only for R 3.1.x.

New update

Package photobiology version 0.3.9 is now available. This update adds summary() methods for spectral objects and a function stepsize() that returns the range of wavelength steps in a spectrum. The source.spct class has gained a "time.unit" attribute, requiring also a change to setSourceSpct(). All these changes and additions are backwards compatible. A probably harmless bug in setSourceSpct() was fixed. The User Guide was edited to reflect these changes. Source package, and Windows binaries for R 3.0.x and 3.1.x were uploaded today.

New update

Package photobiology version 0.3.8 is now available. This is a rather minor update that continues the switch to use of data.table based objects. There are also a few bug fixes and code optimizations. Source package, and Windows binaries for R 3.0.x and 3.1.x were uploaded today.