photobiology

Package ‘photobiology’ defines a system of classes for storing spectral data and accompanying metadata. For each of these classes specialised summary methods, maths operators and functions are provided. In addition, classes for storing collections of objects of the classes for individual spectra are defined as well as ‘apply’ functions. Extraction and replacement operators are implemented.

Functions for calculation of the position of the sun, times of sunrise and sunset, day length and night length are also available. Starting from ‘photobiology’ 0.12.0 they are imported from package ‘SunCalcMeeus’, which is a spin-off of ’photobiology. If you only use these functions, you can attach or load ‘SunCalcMeeus’ instead of ‘photobiology’, otherwise, the only visible change is that the on-line help is at a separate site.

Functions for the estimation of evapotranspiration and the energy balance of vegetation have been migrated to package ‘photobiologyPlants’ as they are related to vegetation. To use them with this version of package ‘photobiology’, please, add library(photobiologyPlants) to your code.

The package supports storage and manipulation of data for radiation quantities and for optical properties of objects and solutes, as well as response and action spectra for photobiological, photochemical and photoelectrical responses.

This package is the core of a suite of R packages for photobiological calculations described at the r4photobiology web site and in the vignette The R for Photobiology Suite.

Examples

The first example shows you how to estimate solar irradiance in W/m2 under a filter. We use a measured solar spectrum and a measured filter transmission spectrum.

library(photobiology)
e_irrad(sun.spct * yellow_gel.spct)
#>  E_Total 
#> 146.5053 
#> attr(,"time.unit")
#> [1] "second"
#> attr(,"radiation.unit")
#> [1] "total energy irradiance"

The second example shows some simple astronomical calculations for the sun.

geocode <- data.frame(lon = 0, lat = 55)
date <- lubridate::now(tzone = "UTC")
sunrise_time(date, tz = "UTC", geocode = geocode)
#> [1] "2025-01-12 08:18:17 UTC"
day_length(date, tz = "UTC", geocode = geocode)
#> [1] 7.670362

Installation

Installation of the most recent stable version from CRAN:

install.packages("photobiology")

Installation of the current unstable version from R-Universe CRAN-like repository:

install.packages('photobiology', 
                 repos = c('https://aphalo.r-universe.dev', 
                           'https://cloud.r-project.org'))

Once package ‘photobiology’ is installed, installation of the remaining or missing packages in the suite from CRAN (or by adding the repository information as above, from R-Universe):

intalled_pkgs <- installed.packages()[ , 1]
missing_pkgs <- setdiff(photobiology::r4p_pkgs, intalled_pkgs)
if (length(missing_pkgs) > 0) {
 install.packages(missing_pkgs)
}

Installation of the current unstable version from GitHub:

# install.packages("devtools")
devtools::install_github("aphalo/photobiology")

Documentation

HTML documentation is available at (https://docs.r4photobiology.info/photobiology/), including three User Guides.

News on updates to the different packages of the ‘r4photobiology’ suite are regularly posted at (https://www.r4photobiology.info/).

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://hdl.handle.net/10138/37558).

Contributing

Pull requests, bug reports, and feature requests are welcome at (https://github.com/aphalo/photobiology).

Citation

If you use this package to produce scientific or commercial publications, please cite according to:

citation("photobiology")
#> To cite package ‘photobiology’ 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},
#>   }

License

© 2012-2025 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.