About

Aims

This web site is the home of software written Pedro J. Aphalo, using the R programming language. It provides news and documentation for the packages and occasional posts on R-related subjects.

The 11 R packages in the r4photobiology suite 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 “reproducible and open science” all the code is open-source and all algorithms and data used, unless original, are linked to the original sources.

Two packages extend ‘ggplot2’ supporting insets and model-fit-based annotations and the manipulation and exploration of ggplot objects.

A package to accompany the book Learn R …as you learnt your mother tongue contains data sets and scripts used in the book.

Scope and organization

The site is divided into a blog containing short posts with news and comentaries, 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 in the analysis and acquisition of data in the field of photobiology as well as in relation to data analysis and plotting in general. 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.

The code for the packages

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 are compatible with Windows (x86/x64), Linux (x86/x64), and OS X. As most packages have been published through the CRAN repository they are regularly checked under multiple OSs.

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/

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. https://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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