About

Aims

This web site is the home of software written Pedro J. Aphalo, using the R programming language. 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), except for those packages in CRAN which have been tested as part of the submission process in all R platforms.

The packages have been designed trying to make code maintenance as simple and as reliable as possible. 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 git repositories at https://bitbucket.org/aphalo/

Scope and organization

The site is divided into a blog containing short posts with news, which are revised only in case they contain errors, and pages with content of long term usefulness, which are updated regularly as needed.

In the blog we publish news related to the use of R, the environment for data analysis and the scripting and programing language, in the analysis and acquisition of data from the field of photobiology. We take a very broad view of photobiology, so anything useful to a photobiologist is within scope. This includes analysis of data that is in the realm of radiation meteorology and climatology, and even geophysics. Contributions from anybody are warmly welcome, but acceptance is at the discretion of the editor.

The site also contains pages with tips on using R for reproducible research and other bits of information related to data analysis and programming with R, including occasional informal reviews of books on R that I have read and R packages that I use.

Citing posts and pages

The following citation is for the whole site:

Aphalo, Pedro J., editor (2013-2018) Using R for Photobiology, https://www.r4photobiology.info. ISSN 2343-3248, Helsinki.

The author and date of first posting is displayed for each post at the top, as well as the URL below the post, so an example citation could be:

Aphalo, Pedro J. (2018) R 3.5.0 and spaces in file paths. http://www.r4photobiology.info/news/ggpmisc-adds-new-stats-to-ggplot2/ ISSN 2343-3248, Helsinki. Visited on 2018-05-25.

Publisher and place of publication

Publisher and editor: Pedro J. Aphalo

Place of publication: Helsinki, Finland.

 

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