R for Photobiology
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R for Photobiology

Theory and recipes for common calculations

About the Book

This handbook describes how to use R as a tool for doing calculations related to research in photobiology. Photobiology is the branch of science that studies the interactions of living organisms with visible and ultraviolet radiation. 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 related to radiation quantification and the position of the sun. These include acquisition, processing and summarising of spectral data including the calculation of non-weighted and biologically effective exposures. Calculations related to interactions of radiation with inanimate objects and organisms are also treated in detail.

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.

In most of the examples we use of a suite of R packages developed by Pedro J. Aphalo and described at http://www.r4photobiology.info/. At the moment the ten most important packages in the suite are available through CRAN and the few remaining ones through a CRAN-like repository at http://r.r4photobiology.info/.

About the Authors

Pedro J. Aphalo
Pedro J. Aphalo

I started using R in the late 1990's for the analysis of data from my own experiments. Shortly afterwards in 2001, I started teaching R at BSc and MSc level at the University of Jyväskylä (Finland). I have developed several R packages of which nine are in CRAN , the public repository of R packages. Over the years I have written programs and scripts in about a dozen different languages.

I am currently a Lecturer in Physiological Plant Ecology and Principal Investigator at the Department of Biosciences of the University of Helsinki (Finland). The main focus of my research in on the study of the mechanisms of acquisition and use of information by plants: a field called 'Sensory Ecology of Plants'. I teach ecology, statistics and methods for reproducible research.

My R packages are described at http://www.r4photobiology.info/ and my research in plant biology at http://blogs.helsinki.fi/senpep-blog/

T. Matthew Robson
T. Matthew Robson

I head a research group in Canopy Spectral Ecology and Ecophysiology (CanSEE) at the University of Helsinki.  My principal focus is on changes in the spectrum of radiation penetrating forests canopies with latitude & its influence on the understorey. My expertise is on the biological effects of UV radiation and on understanding the effects of climate change on forests. 

Currently there is a revolution in canopy research made possible by technologies that allow remote sensing of forest canopies from the air (through drones, photos, and satellites) coupled with a new generation of radiation sensors to transmittance, reflectance, fluorescence and irradiance. Our research utilises these state-of-the-art tools in biophysics to assess the real-time penetration of sunlight through canopies and scale-up the assessment of canopy processes along a climatic and latitudinal gradient stretching from Spain to Lapland.  

Titta Kotilainen
Titta Kotilainen

I used R during my PhD studies on the photobiology of plants. Afterwards I continued using this software for all the analysis of data I have come across. My specialities are solar and artificial radiation and their effects on plants. I have been applying my knowledge in the field of artificial lighting in horticulture as a research manager for Valoya. Currently I am working as a researcher at the Department of Biosciences of the University of Helsinki (Finland), in a group focusing on canopy spectral ecology and ecophysiology. I also own a research consultancy and data analysis services company called Radiantik.

About the Contributors

Andreas Albert
Andreas Albert


Table of Contents


Part I Theory behind calculations

1 Radiation properties

2 Radiation interactions

3 Photochemistry and photobiology

4 Algorithms

Part II Tools used for calculations

5 Software

6 Photobiology R packages

Part III Cockbook of claculations

7 Arithmetic operators and mathematical fucntions

8 Spectra: simple summaries and features

9 Wavebands: simple summaries and features

10 Irradiance (not weighted)

11 Irradiance (weighted or effective)

12 Transmission and reflection

13 Astronomy (of the sun)

14 Colour

15 Colour-based indexes

16 Plotting spectra and colours

17 Radiation physics

Part IV Data Acquisition and exchange

18 Importing and exporting 'R' data

19 Importing and exporting 'foreign' data

20 Data acquisition from within R

21 Calibration

22 Simulation

Part V Catalogue of example data

23 Radiation sources

24 Optical properties of inanimate objects

25 Example data for organisms

26 Further reading



VI Appendix

A Build information

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