photobiologyPlants

Package ‘photobiologyPlants’ provides pre-defined functions for quantifying visible (‘VIS’), near infra-red (‘NIR’) and ultraviolet (‘UV’) radiation in relation to their effects on plants together with action spectra for photosynthesis and absorbance spectra for the plant photoreceptors in families ‘phytochromes’, ‘cryptochromes’, ‘zeitlupe proteins’, ‘phototropins’ and ‘UVR8s’ which are present in plants. It also includes data sets on the optical properties of plant organs, photosynthesis and plant pigments, chlorophylls and carotenoids. All data are derived from the scientific literature. Please, see the help pages for the different data sets for details about the sources used.

The data in this package are stored in objects of classes defined in package ‘photobiology’ which are mostly backwards compatible with data frames.

This package is part of a suite of R packages for photobiological calculations described at the r4photobiology web site.

Examples

library(ggspectra)
library(photobiologyPlants)

We plot the action spectrum of photosynthesis in Oats.

comment(McCree_photosynthesis.mspct$oats)
#> [1] "One of the 'classical' action spectra of K. J. McCree (1972) Avena sativa L. var. Coronado."

class(McCree_photosynthesis.mspct$oats)
#> [1] "response_spct" "generic_spct"  "tbl_df"        "tbl"          
#> [5] "data.frame"

autoplot(McCree_photosynthesis.mspct$oats, 
         annotations = c("+", "title:none:what"))

We can calculate the R:FR photon ratio of a spectrum, in this case an example solar spectrum at ground level from package ‘photobiology’.

R_FR(sun.spct)
#> R:FR[q:q] 
#>  1.266704 
#> attr(,"radiation.unit")
#> [1] "q:q ratio"

We can also estimate the photo-equilibrium of phytochrome exposed in vitro to the same spectrum.

Pfr_Ptot(sun.spct)
#> [1] 0.68341

Installation

Installation of the most recent stable version from CRAN:

install.packages("photobiologyLamps")

Installation of the current unstable version from Bitbucket:

# install.packages("devtools")
devtools::install_bitbucket("aphalo/photobiologylamps")

Documentation

HTML documentation is available at (https://docs.r4photobiology.info/photobiologyPlants/), including a User Guide.

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/photobiologyPlants).

Citation

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

citation("photobiologyPlants")
#> To cite package 'photobiologyPlants' in publications, please 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

© 2015-2023 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.