photobiology 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 Kotilainen, 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.

Please, be aware that future updates will be announced by posting only at the r4phobiology blog and in this UV4growth blog only the RSS feed will be shown as widget. You can yourself also subscribe to the RSS feed to be notified of the updates.

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Data on filters and glasses available on-line

Download Library: SCHOTT Advanced Optics | SCHOTT AG.

Download Library: SCHOTT UK (lab glassware)

Download Library: SCHOTT (tubing)

ABRISA catalogue with data on many different types of glasses.

This can be very useful, for example when looking for a suitable filter or window material.

Posted in Equipment, Filters | Leave a comment

R packages for photobiology updated

The packages described in the previous post have been tested and updated. A new package photobiologyCry has been added for calculations related to CRY or cryptochromes. The sources are at  https://bitbucket.org/aphalo/photobiologyphy. The new source and windows binaries (x86 and x64) packages can be downloaded  https://bitbucket.org/aphalo/photobiology

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R packages for photobiology

I am developing a new set of R packages for us in photobiology, in particular for quantifying radiation. There is a “beta” version available for testing at https://bitbucket.org/aphalo/photobiology (all built source and binary downloads, and repository of base package for photobiology), https://bitbucket.org/aphalo/photobiologyuv (ultraviolet package), https://bitbucket.org/aphalo/photobiologyvis (visible package) and https://bitbucket.org/aphalo/photobiologyphy (phytochrome package). The Bitbucket repositories are public, so you can suggest changes to the code, etc. This package will soon replace package UVcalc. Package photobiology already implements all the functionality of UVcalc, but using a different user interface.

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Handbook PDF download working again

The download links to the PDF files of the handbook were pointing to an address that was no longer in use. I edited the links to the HANDBOOK page to point to the new location of the files.

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UVcalc update

There was a minor update available in Bitbucket that I didn’t announce. It was version 1.0.7 which added a NAMESPACE for compatibility with R 3.0.0 and had byte compilation enabled to improve performance.

I did some work during the last couple of weeks and I pushed to Bitbucket version of UVcalc 1.2.1. This version is backwards compatible in every respect except the output. The packaged source and the binary package for R 3.0.x and R 2.15.x for Windows as a .zip files are available at Bitbucket for download. Please, read also the Reame.txt file at  Bitbucket, it contains important information on installation.

The interpolation algorithm has been improved to better cope with BSWFs that are not continuous or smooth along wavelengths. For solar spectral data at 1 nm interval, the change in most cases affects only the fourth significant digit, but in a few cases, the new more exact values may differ from those calculated with the previous version by as much as 3%. I haven’t done any tests with spectra measured using wider wavelength steps, but I would expect the improvement to be more important.

I have still a few improvements in mind, mainly a few additional functions to complement those already in the package. Improved documentation is also planned, although I have added some new examples in version 1.2.0.

As always, please report any problems or errors that you find, or tell me what improvements or additions you would find useful.

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Some links on units and measurements

View the Measurements, units and errors notebook on Springpad

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