About

This blog is the home of software written Pedro J. Aphalo, using the S and C++ programming languages. The different R packages implement calculations related to handling of spectral data as used in photobiology. The main purpose of this software is to make it easier for biologists to quantify and describe the visible and ultraviolet radiation conditions used in experiments or monitored in nature, in a standardized and consistent way. In accordance with the ideas of “repeatable science” all the code is open-software and all algorithms and data used, unless original, are linked to the original sources. The code is fully commented and written using consistent naming conventions and a consistent formatting style. The packages are fully documented and include usage examples for all functions. Documentation follows standard R documentation practices, and includes several vignettes, including user manuals. The packages should be compatible with Windows (x86/x64), Linux (x86/x64), and OS X. Testing has been done under Ubuntu (64 bit)  and Windows (32/64 bit).

The packages have been designed trying to make code maintenance as simple and as reliable as possible. There is not a single line of duplicate code in the whole set of packages. A couple functions involving for loops that could not be vectorized using S language constructs have been coded in C++ using the Rcpp packaage.

Furthermore, a central aim of the design has been to allow the easy implementation of additional ways of quantifying radiation by users, who will hopefully contribute them back to this project so that this family of packages with time caters for all aspects of photobiology.

The latest source code and all earlier versions are available from repositories at Bitbucket.org

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