photobiology-package
photobiology: Photobiological Calculations
Description
Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Details
Package 'photobiology' is at the core of a suite of packages for analysis and plotting of data relevant to photobiology (described at https://www.r4photobiology.info/). The accompanying packages (under development) provide data and definitions that are to a large extent application-area specific while the functions in the present package are widely useful in photobiology and radiation quantification in geophysics and meteorology. Package 'photobiology' has its main focus in the characterization of the light environment in a biologically relevant manner and in the manipulation of spectral data to simulate photo-physical, photo-chemical and photo-biological interactions and responses. The focus of package 'pavo' (Maia et al., 2003) is in colour perception by animals and assessment of animal coloration. In spite of the different focus, there is some degree of overlap.
Acknowledgements
This work was funded by the Academy of Finland (decision 252548). COST Action FA9604 'UV4Growth' facilitated discussions and exchanges of ideas that lead to the development of this package. The contributions of Andy McLeod, Lars Olof Björn, Nigel Paul, Lasse Ylianttila, T. Matthew Robson and Titta Kotilainen were specially significant. Tutorials by Hadley Wickham and comments on my presentation at UseR!2015 allowed me to significantly improve the coding and functionality.
Note
Code for some of the astronomical calculations has been adapted from that in package 'pavo'.
Author(s)
Maintainer: Pedro J. Aphalo pedro.aphalo@helsinki.fi (ORCID)
Other contributors:
-
Titta K. Kotilainen (ORCID) [contributor]
-
Glenn Davis gdavis@gluonics.com [contributor]
-
Agnese Fazio agnese.fazio@uni-jena.de [contributor]
References
Aphalo, P. J., Albert, A., Björn, L. O., McLeod, A. R., Robson, T. M., Rosenqvist, E. (Eds.). (2012). Beyond the Visible: A handbook of best practice in plant UV photobiology (1st ed., p. xx + 174). Helsinki: University of Helsinki, Department of Biosciences, Division of Plant Biology. ISBN 978-952-10-8363-1 (PDF), 978-952-10-8362-4 (paperback). Open access PDF download available at https://hdl.handle.net/10138/37558
Aphalo, Pedro J. (2015) The r4photobiology suite. UV4Plants Bulletin, 2015:1, 21-29. doi: 10.19232/uv4pb.2015.1.14.
Maia, R., Eliason, C. M., Bitton, P. P., Doucet, S. M., Shawkey, M. D. (2013) pavo: an R package for the analysis, visualization and organization of spectral data. Methods in Ecology and Evolution, 4(10):906-913. doi: 10.1111/2041-210X.12069.
See Also
Useful links:
Examples
# irradiance of the whole spectrum
irrad(sun.spct)
# photon irradiance 400 nm to 700 nm
q_irrad(sun.spct, waveband(c(400,700)))
# energy irradiance 400 nm to 700 nm
e_irrad(sun.spct, waveband(c(400,700)))
# simulating the effect of a filter on solar irradiance
e_irrad(sun.spct * yellow_gel.spct, waveband(c(400,500)))
e_irrad(sun.spct * yellow_gel.spct, waveband(c(500,700)))
# daylength
sunrise_time(lubridate::today(tzone = "EET"), tz = "EET",
geocode = data.frame(lat = 60, lon = 25), unit.out = "hour")
day_length(lubridate::today(tzone = "EET"), tz = "EET",
geocode = data.frame(lat = 60, lon = 25), unit.out = "hour")
# colour as seen by humans
color_of(sun.spct)
color_of(sun.spct * yellow_gel.spct)
# filter transmittance
transmittance(yellow_gel.spct)
transmittance(yellow_gel.spct, waveband(c(400,500)))
transmittance(yellow_gel.spct, waveband(c(500,700)))