Training at Luke Suonenjoki

We will use this page to keep links to material to be used in the event, previous reading and further readings.

Books and handbooks authored by the teachers

Two of these books are for sale at Leanpub, but with a minimum price of zero. As Luke is paying for this training event, please, do not hesitate to move the price slider to “FREE” before downloading them. They are work in progress, and by registering with Leanpub we will be able to let you know when we upload revised versions. Please, feel free to share this links.

R for Photobiology: Theory and recipes for common calculations

Cover image.
“R for Photobiology”
(Preprint 2016)

R for Photobiology describes how to use R as a tool for doing calculations related to research in photobiology. Many of the most frequently used calculations are either related to the characterization of radiation and of the responses of organisms to radiation. We emphasize the first of these aspects as in many cases the characterization of the responses of organisms to radiation differ little from the characterization of similar responses elicited through other physical or chemical stimuli.Many of the examples in this handbook make use of the `r4photobiology’  suite of R packages, but the use of other packages is also described.

The text and examples assume some familiarity with R and/or programming, but guides those readers new to the language to tutorials and books that will help them learn enough to follow, use and modify the code examples included in the book. The book is structured in five parts: I Theory behind calculations, II Tools used for calculations, III Cookbook of calculations, IV Data acquisition and exchange and V Catalogue of example data.

Learn R …as you learnt your mother tongue

Book cover
Learn R (preprint 2016)

Learn R covers different aspects of the use of the R language plus the languages behind some R packages, such as the grammar of graphics implemented in package ‘ggplo2’. I do not discuss here statistics, just R as a tool and language for data manipulation and display. The idea is for you to learn the R language like children learn a language: they work-out what the rules are simply by listening to people speak and trying to utter what they want to tell their parents. I do give some explanations and comments, but the intention is mainly for you to use the numerous examples to find-out by yourself the overall patterns and coding philosophy behind the R language. Instead of parents being the sound board for your first utterances in R, the computer will play this role. You should look at and try to repeat the examples, and then try your own hand at modifying them and see how the computer responds, does it understand you or not? Then write something new based on your current understanding of the rules…

Learn the R language as a child would: Do not struggle, just play! If going gets difficult and frustrating, take a break! If you get a new insight, take a break to enjoy the victory!

Beyond the Visible : A handbook of best practice in plant UV photobiology

Image of front cover
Beyond the Visible (1ed, 2012)

Beyond the Visible: A handbook of best practice in plant UV photobiology presents methods for research on the responses of plants to ultraviolet (UV) radiation. The knowledge needed to make informed decisions about manipulation and quantification of UV radiation is summarized. Practical recommendations for obtaining reliable and relevant data and interpretations are given. The handbook covers research both on terrestrial and aquatic plants and it deals with experimentation on ecological, eco-physiological and physiological questions. The handbook includes 115 figures, mostly in colour, 19 tables and 12 text boxes. It is the result of the activities of COST action FA0906 “UV4growth”, and it includes contributions by 17 authors.

Printed version is available through Amazon, the PDF is under open-access at hdl:10138/37558

 The r4photobiology website

Do explore this site, and when using the suite of R packages for photobiology, check the on-line documentation at http:/

Lectures introducing R (slides)

what_is_r1) What is R?

 2) R as a scripting language (first part)R1_Page_01
 3) R as a scripting language (second part)R2

Using RStudio

Video for getting started with photobiology packages.
Video for getting started with photobiology packages.