Aphalo P. R for Photobiology. A handbook of theory and computations 2022

Textbook in PDF format

Photobiology is the branch of science that studies the interactions of living organisms with visible and ultraviolet radiation. This book first presents the theory behind calculations related to research in photobiology and describes how to use R as a tool for carrying out these calculations.
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:
Preface
I Theory behind calculations
Typographical conventions
Radiation interactions
Photochemistry and photobiology
Algorithms
II Tools used for calculations
Software
R for Photobiology packages
III Cookbook of calculations
Storing data
Arithmetic operators and mathematical functions
Spectra: simple summaries and features
Wavebands: simple summaries and features
Irradiance (not weighted)
Irradiance (weighted or effective)
Transmission and reflection
Astronomy
Colour
Colour based indexes
Plotting spectra and colours
Radiation physics
IV Data acquisition and exchange
Importing and exporting ‘R’ data
Importing and exporting ‘foreign’ data
Data acquisition from within R
Calibration
Simulation
V Catalogue of example data
Radiation sources
Optical properties of inanimate objects
Example data for organisms
VI Appendix