Home page

A brief presentation of the site


The best way to remain up-to-date about the contents of this site is to use an RSS feed reader such as NetNewsWire (iPhone) or a browser add-on like “FeedBro” (Firefox) and subscribe to the feeds you are interested in. The RSS entry in the site’s main menu contains links to three separate feeds, for the Blog, Pages and R Gallery sections of the website.

I publish occasionally announcements through Mastodon. I use hashes to differentiate posts by subject so that you can follow what you are interested in without cluttering your Mastodon Home. You can see my first post through Mastodon or my first toot.

You can visit my Mastodon profile at https://mastodon.social/@aphalo. I am no longer using Twitter/X or Facebook.

1 Contents

The following sections of the site can be accessed through the menu at the top of all pages in the website. The most recent content is also showcased below.

The contents can be accessed through four tables of contents: blog post, pages, R gallery and a selection of material on R and data analysis that I have used in teaching course or advice to students at BSc, MSc and PhD levels.

1.1 Blog

The blog contains short articles, mostly news that once published are not revised, or revised during a few months, except for mistakes. In this section I published condensed news about package updates, and books and articles published elsewhere.

1.2 Pages

The pages are informative articles and tutorials that once published are updated as needed to keep them useful and relevant. Many of the pages are based on material prepared for courses or talks and republished in a different format. In general, the focus is not on cookbook-style R code examples.

1.4 R packages

This menu entry gives access to the documentation in HTML format for all the R packages that I actively maintain. It also lists a page that summarizes the results of the latest test runs at CRAN and GitHub and links for reporting bugs or requesting support.

I also maintain a CRAN-like repository with those packages that I maintain but which are not available through CRAN. Occasionally, I also make available under development versions of the packages that are available through CRAN through this repository.

1.5 Books

This menu entry gives access to pages related to books I have written or edited about R and/or photobiology.

1.6 Data

Here you will find data acquired at a weather station that I manage. The station is located in the Viikki Campus of the University of Helsinki, in Helsinki, Finland. There is also a description of the station equipment and the variables in the data.

1.7 About

Pages with additional information about the site and its webmaster and author.

2 R, data analysis and photobiology

This website’s focuses mostly on methodology, and R and R packages as tools. It complements R packages and books I have authored. The site emphasizes the use of the R packages I have developed and maintain, including extensions to ‘ggplot2’ and a suite of several R packages supporting computations, data acquisition and plotting related to photobiology. However, this website also includes some content broadly applicable to data analysis and data visualization.

autoplot(sun.daily.spct, annotations = c("+", "title:where:when"))

3 My other websites

I have been using and teaching R, the free software environment for statistical computing and graphics, for more than 20 years. I am a researcher working in the field of sensory ecology of plants. I have been interested throughout my career in plants’ responses to light.

In my research group we have used R for general data analysis, as well as for plotting and calculations related to photobiology. As a result of all these activities I developed several R packages and published them through CRAN. I have also written books both on R and on photobiology.

I have a separate website for my research group’s activities and a website with material related to photography and photography techniques. My scientific publications are listed at my ORCID profile.

I published my first website, The Plant Photobiology Notes, between 1995 and 2001. Initially it was hosted in the desktop PC in my office, the same I used everyday for other tasks. The site survived with minor updates, mostly deletion of broken links, until around 2009. In the meantime the URL changed two or three times when I changed jobs. Much of its contents are now outdated but the site was archived by the Wayback Machine and remains available. Most of the spectral data at the old site are now included in my R packages together with newer data.