photobiology (version 0.11.3)

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) tools:::Rd_expr_doi("10.19232/uv4pb.2015.1.14").

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.

Author

Maintainer: Pedro J. Aphalo (ORCID)

Other contributors:

• Titta K. Kotilainen (ORCID) [contributor]

• Glenn Davis [contributor]

• Agnese Fazio [contributor]

Details

Package ‘photobiology’ is at the core of a suite of R packages supporting computations and plotting relevant to photobiology (described at https://www.r4photobiology.info/). Package 'photobiology' has its main focus in the characterization of the light environment, the description of optical properties of objects and substances and description of light responses of organisms and devices used to measure light. The facilities for spectral data storage and manipulations are widely useful in photobiology, chemistry, geophysics, radiation climatology and remote sensing. Astronomical computations for the sun are also implemented. The design of object classes for spectral data supports reproducibility by facilitating the consistent use of units and physical quantities and consistent embedding of metadata. Data are expressed throughout using SI base units, except for wavelengths which are consistently expressed in nanometres [\(nm\)]. Please see the vignette 0: The R for Photobiology Suite for a description of the suite.

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 tools:::Rd_expr_doi("10.31885/9789521083631").

Aphalo, Pedro J. (2015) The r4photobiology suite. UV4Plants Bulletin, 2015:1, 21-29. tools:::Rd_expr_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. tools:::Rd_expr_doi("10.1111/2041-210X.12069").

See Also

Useful links:

• https://docs.r4photobiology.info/photobiology/

• https://github.com/aphalo/photobiology

• Report bugs at https://github.com/aphalo/photobiology/issues

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)))