R for Photobiology
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/.
Part I Theory behind calculations
1 Radiation properties
2 Radiation interactions
3 Photochemistry and photobiology
Part II Tools used for calculations
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)
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
Part V Catalogue of example data
23 Radiation sources
24 Optical properties of inanimate objects
25 Example data for organisms
26 Further reading
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