Scope and organization
This site is divided into sections, with separate lists of contents. The R for Photobiology section is the home of software written Pedro J. Aphalo, using the R programming language. This section provides news, documentation and use examples for the packages and occasional posts on R-related and photobiology-related subjects.
I have lately added content related to courses that I have taught on R and data analysis, transferred still relevant posts from the SenPEP blog and material from seminar and congress presentations.
The site contains short posts with news (revised only in case they contain errors), pages with content of longer term usefulness (updated as needed) and galleries with “cookbook” style collections of use examples for R and R packages (also updated as needed).
In the site I publish contents 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. Most frequently, blog posts describe updates to R packages. Overall contents is related to photobiology, agriculture, radiation meteorology and climatology, and data analysis and data visualization. Contributions from anybody are warmly welcome, but acceptance is at the discretion of the editor.
How the site is built and served
For nearly 10 years the (https://www.r4photobiology/) web site was hosted on a WordPress server that dynamically serves pages built from the content of a data base. Currently the pages in the site are static, served from files generated off-line using Quarto. Quarto converts Rmarkdown encoded source files into an HTML website. The HTML rendering chain is based on R, knitr, and Pandoc. The markdown sources can include code chunks that are run when the site is rendered into HTML.
A significant drawback of the move was that post and page URLs have not been preserved. However, the new built-in search works well and fast, based on a static index. During the transfer of contents from WordPress is removed announcements and other old content that was no longer relevant. This was also the case for content moved from the SenPEP blog hosted at the University of Helsinki’s WordPress server.
Citing posts and pages
The following citation is for the whole site:
Aphalo, Pedro J., editor (2013-2024) Using R for Photobiology, https://www.r4photobiology.info/, ISSN 2343-3248, Helsinki.
The author and date of first posting are displayed for each post under the title, so an example citation could be:
Aphalo, Pedro J. (2018) Using the Quick TUV Calculator: Importing simulated solar spectrum data into R. https://www.r4photobiology.info/galleries/QuickTUV.html ISSN 2343-3248, Helsinki. Visited on 2024-09-15.
Publisher and place of publication
Publisher and editor: Pedro J. Aphalo
Place of publication: Helsinki, Finland.
Hosting service
This site has been hosted for many years, and continues being hosted after the recent migration to Quarto, by Webbinen which I can only praise and recommend. Support has been incredibly knowledgeable, efficient and fast, every single time I have contacted them over these years. All my sites have worked without a glitch all this time.