https://github.com/aphalo/photobiologyplants

R package part the R for Photobiology suite

https://github.com/aphalo/photobiologyplants

Repository

R package part the R for Photobiology suite

README.Rmd

---
output:
  github_document
---

```{r readme-01, echo = FALSE}
knitr::opts_chunk$set(
  fig.asp = 2/3,
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
```

# photobiologyPlants 


[![CRAN version](https://www.r-pkg.org/badges/version-last-release/photobiologyPlants)](https://cran.r-project.org/package=photobiologyPlants) [![cran checks](https://badges.cranchecks.info/worst/photobiologyPlants.svg)](https://cran.r-project.org/web/checks/check_results_photobiologyPlants.html) 
[![R Universe vwersion](https://aphalo.r-universe.dev/badges/photobiologyPlants)](https://aphalo.r-universe.dev/photobiologyPlants)
[![R build status](https://github.com/aphalo/photobiologyPlants/workflows/R-CMD-check/badge.svg)](https://github.com/aphalo/photobiologyPlants/actions)
[![Documentation](https://img.shields.io/badge/documentation-photobiologyPlants-informational.svg)](https://docs.r4photobiology.info/photobiologyPlants/)
[![doi](https://img.shields.io/badge/doi-10.32614/CRAN.package.photobiologyPlants-blue.svg)](https://doi.org/10.32614/CRAN.package.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. Absorbance spectra for the plant photoreceptors in families
'phytochromes', 'cryptochromes', 'zeitlupe proteins', 'phototropins' and
'UVR8s' are included together with absorbance spectra for plants' "mass pigments",
including chlorophylls, carotenoids and some other metabolites such as flavonoids.

The package also includes data sets on the optical properties of plant organs,
including whole-leaf reflectance, absorptance, transmittance and 
fluorescence spectra. 

All data are derived from the scientific literature. Please, see the help pages
for the different data sets for details about the primary sources of the data.

The package includes functions for the calculation of reference 
evapotranspiration using different approaches, for unit conversions for water in 
the atmosphere and for the computation of the energy balance of vegetation. 
These functions were included in package 'photobiology' (< 0.12.0) and have been
migrated to 'photobiologyPlants' (>= 0.6.0).

The data in this package are stored in objects of classes defined in package 
'**photobiology**' which are mostly backwards compatible with data frames but
include metadata as attributes.

This package is part of a suite of R packages for photobiological calculations 
described at the [r4photobiology](https://www.r4photobiology.info) web site.

## Examples

```{r, message=FALSE}
library(photobiologyPlants)
eval_plots <- requireNamespace("ggspectra", quietly = TRUE)
if (eval_plots) library(ggspectra)
```

Spectral data are stored in R objects of classes defined in package 
'photobiology'.

```{r}
class(McCree_photosynthesis.mspct$oats)
```

Objects contain metadata that can be queried. The `comment` attribute
commonly used in R.

```{r}
comment(McCree_photosynthesis.mspct$oats)
```

And also other attributes defined in package 'photobiology'.

```{r example2}
what_measured(McCree_photosynthesis.mspct$oats)
how_measured(McCree_photosynthesis.mspct$oats)
is_normalised(McCree_photosynthesis.mspct$oats)
```

Functions defined in package 'ggspectra' make plotting easy. For example, to
plot the action spectrum of photosynthesis in Oats we can use.

```{r, eval=eval_plots}
autoplot(McCree_photosynthesis.mspct$oats, unit.out = "photon")
```

We can calculate the R:FR photon ratio of a light-source or iradiance spectrum,
in this case the solar spectrum at ground level measured on at a specific
location and time, included in package 'photobiology'.

```{r}
R_FR(sun.spct)
```

We can also estimate the photo-equilibrium of phytochrome exposed _in vitro_ to the same spectrum. 

```{r}
Pfr_Ptot(sun.spct)
```

## Installation

Installation of the most recent released version from CRAN (source and binaries available):

```{r, eval=FALSE}
install.packages("photobiologyLamps")
```

Installation of the current unstable version from R-Universe CRAN-like repository (source and binaries available):

```{r, eval=FALSE}
install.packages('photobiologySun', 
                 repos = c('https://aphalo.r-universe.dev', 
                           'https://cloud.r-project.org'))
```

Installation of the current unstable version from GitHub (only source available):

```{r, eval=FALSE}
# install.packages("remotes")
remotes::install_github("aphalo/photobiologylamps")
```

## Documentation 

HTML documentation is available at (https://docs.r4photobiology.info/photobiologyPlants/), including the _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:

```{r citation}
citation("photobiologyPlants")
```

## License

© 2015-2025 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.

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