Package ‘photobiologyWavebands’ supplies a set of functions and data to
be used together with package ‘photobiology’ for calculation of derived
quantities from spectral data. Package ‘photobiology’ defines class
waveband for storing wavelength ranges or spectral weighting functions
plus wavelength ranges and a corresponding constructor function
waveband(). Package ‘photobiologyWavebands’ provides specialized
contructors so that frequently used wavebands can be created by name
instead of directly entering numeric boundaries for wavelength and
user-defined functions for weighting as needed when using waveband().
R functions for computing frequently used spectral weighting factors for
arbitrary wavelengths in nanometres are also exported. These functions
are the basis for the computation of (biologically) effective spectral
irradiances and irradiances.
Non-weighted derived quantities represent summaries of a given range of
wavelengths, i.e., weight is 1 irrespective of wavelength or use of
photon or energy units. In this case constructors of waveband objects
default to ISO standardized definitions when they are available, with
other competing definitions available by passing character strings as
argument to parameter std.
The non-weighted definitions cover most non-weighted wavebands in common use, like those corresponding ultraviolet, visible and infrared, the light colours seen by humans, and some other bands of interest for plants.
Several wavebands corresponding to remote sensing instruments are also provided, including all those for the LANDSAT and Sentinel-2 missions, as non-weighted definitions. The Sentinel-2 multi spectral imager (MSI) bands are available as a central wavelength plus band width. For the Landsat imagers specific responsiveness vs. wavelength data are available, and could in principle have to be defined using response-dependent weighting functions. The calibrations and definitions provided by NASA are based on average response per band. If Landsat or Sentinel-2 response bands are to be simulated very accurately using spectral data from other, possibly terrestrial, instruments these approximations need consideration. In other cases, the approximation using a simple wavelength range, as provided in this package, can be good enough, because this is a rather good approximation to the actual responsivity curve.
The definition of photosyntheticaly active radiation (PAR) is non-weighted on a photon basis but spectrally weighted on an energy based. In some cases the same range of wavelengths as in the definition of PAR is used to compute a non-weighted energy irradiance, which should in principle not be called PAR because of the different weighting! In this R package, the name PhR (photosynthetic radiation) is used instead of PAR for energy irradiance in the range 400 to 700 nm.
Both PAR and illuminance are based on biological spectral weighting
functions, approximating the spectral response of photosynthesis and the
human-perceived light brightness, respectively. Several other derived
biologically effective quantities are used to quantify the effect of
radiation on different organisms or processes within organisms. These
effects can range from damage to perception of informational light
signals and cues including vision. Weighting function definitions
represent measurable or expected biological or photocheminal responses,
and consequently they differ if used to compute effective spectral
energy- and photon irradiances. Thus, two versions of weighting
functions are stored in waveband objects.
Exports from ‘photobiologyWavebands’ also include several weighting
functions used for the calculation of the weights used in the
computation of effective irradiances and exposures. These are the same
functions used by constructors of waveband objects. These Weighting
functions are mostly biological spectral weighting functions (BSWFs)
used to estimate effective UV doses. Except for the definition the
erythema (human skin reddening) and vitamin-D3 BSWFs for which
definitions standardized by CIE exist, the default formulation is one
commonly used and/or preferred by the author of the package. It should
be kept in mind that mathematical formulations and extrapolation rules
in use are not unique making it important to carefully chose the most
appropriate ones and to report in full detail which one was used. We
hope this package will make this easier. The estimated summary values
depend strongly on the choice of BSWF, its formulation and the
extrapolation rules used. These choices remain in the hands of users,
expected to have the necessary knowledge.
Colour-response and colour-matching functions for human vision and bee vision are included in package ‘photobiology’. Absorbance spectra for plant photoreceptors and some common plant pigments, as well as action spectra for photosynthesis are included in package ‘photobiologyPlants’. Response spectra for several broad band sensors are included in package ‘photobiologySensors’. Package ‘colorSpec’ provides tools for working with colours, including colour spaces for devices like cameras. Package ‘photobiologyInOut’ facilitates translation of spectral data stored in classes defined in package ‘photobiology’ and other packages such as ‘colorSpec’.
Installation of the most recent stable version from CRAN:
install.packages("photobiologyWavebands")Installation of the current unstable version from R-Universe CRAN-like repository:
install.packages('photobiologyWavebands',
repos = c('https://aphalo.r-universe.dev',
'https://cloud.r-project.org'))The two approaches above, automatically install dependencies.
Installation of the current unstable version from GitHub:
# install.packages("remotes")
remotes::install_github("aphalo/photobiologyWavebands")Installation from GitHub sources does not automatically install dependencies.
HTML documentation is available at (https://docs.r4photobiology.info/photobiologyWavebands/), including an User Guide.
Two articles introduce the basic ideas behind the design of the suite and describe its use: Aphalo P. J. (2015) (https://doi.org/10.19232/uv4pb.2015.1.14) and Aphalo P. J. (2016) (https://doi.org/10.19232/uv4pb.2016.1.15).
A book is under preparation, and the draft is currently available at (https://leanpub.com/r4photobiology/).
A handbook written before the suite was developed contains useful information on the quantification and manipulation of ultraviolet and visible radiation: 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. xxx + 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). PDF file available from (https://doi.org/10.31885/9789521083631).
Pull requests, bug reports, and feature requests are welcome at (https://github.com/aphalo/photobiologyWavebands).
If you use this package to produce scientific or commercial publications, please cite according to:
citation("photobiologyWavebands")
#> To cite package ‘photobiologyWavebands’ in publications use:
#>
#> Aphalo, Pedro J. (2015) The r4photobiology suite. UV4Plants Bulletin,
#> 2015:1, 21-29. DOI:10.19232/uv4pb.2015.1.14
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> author = {Pedro J. Aphalo},
#> title = {The r4photobiology suite},
#> journal = {UV4Plants Bulletin},
#> volume = {2015},
#> number = {1},
#> pages = {21-29},
#> year = {2015},
#> doi = {10.19232/uv4pb.2015.1.14},
#> }© 2012-2026 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.