https://github.com/aphalo/photobiologysensors

Spectral response and other data about light sensors

https://github.com/aphalo/photobiologysensors

Repository

Spectral response and other data about light sensors

README.Rmd

---
output:
  github_document:
    html_preview: TRUE
---

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

# photobiologySensors 


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[![R-CMD-check](https://github.com/aphalo/photobiologySensors/workflows/R-CMD-check/badge.svg)](https://github.com/aphalo/photobiologySensors/actions)
[![Documentation](https://img.shields.io/badge/documentation-photobiologySensors-informational.svg)](https://docs.r4photobiology.info/photobiologySensors/)
[![doi](https://img.shields.io/badge/doi-10.32614/CRAN.package.photobiologySensors-blue.svg)](https://doi.org/10.32614/CRAN.package.photobiologySensors)


  
Package **photobiologySensors** is a collection of spectral responsiveness data
for different broadband sensors and of angular response data for some of the
same sensors and for cosine diffusers and other entrance optics used with
spectrometers. It complements other packages in the suite of R packages for
photobiology 'r4photobiology'. This package contains only data.

## Examples

```{r example-02, message=FALSE}
library(photobiologySensors)
eval_ggspectra <- requireNamespace("ggspectra", quietly = TRUE)
if (eval_ggspectra) library(ggspectra)
```

How many spectra are included in the current version of 'photobiologyFilters'?

```{r example-03}
length(sensors.mspct)
```

What are the names of available spectra? We use `head()` to limit the output.

```{r example-04}
# list names of the first 10 sensors
head(names(sensors.mspct), 10)
```

To subset based on different criteria we can use predefined character vectors of
filter names. For example, vector `licor_sensors` lists the names of the spectra
for sensors from LI-COR.

```{r example-05}
kipp_sensors
```

We can use the vector to extract all these spectra as a collection, or as show
below, extract data for PAR sensors from Kipp.

```{r example-05a}
sensors.mspct[intersect(kipp_sensors, par_sensors)]
```

Please, see the _User Guide_ or help pages for the names of other vectors of
names by supplier, wavelength region and  of the spectrum.
Summary calculations can be easily done with methods from package
'photobiology'. Here we calculate mean photon response for two regions of the
spectrum delimited by wavelengths in nanometres. Roughly 99% of the photons
sensed by this sensor are within PAR.

```{r example-06}
q_response(sensors.mspct[["LICOR_LI_190R"]], 
           list(waveband(c(400, 700)), waveband(c(700, 800))),
           quantity = "contribution")
```

The `autoplot()` methods from package 'ggspectra' can be used for plotting one
or more spectra at a time. The classes of the objects used to store the spectral
data are derived from `"data.frame"` making direct use of the data easy with
functions and methods from base R and various packages.

```{r example-07, eval=eval_ggspectra}
autoplot(sensors.mspct[["LICOR_LI_190R"]])
```

## Code breaking renaming of data objects in 2020

In the update to version 0.5.0 in October 2020 several members of the collection
of sensor-response spectra were renamed to ensure consistency and clarity. As of
version 0.5.0 all member names start with the name of the manufacturer or
supplier. In addition, several of the vectors of names of member spectra were
renamed to include the word "sensors" to avoid possible name clashes with other
packages and also to improve naming consistency.

## Installation

Installation of the most recent stable version from CRAN:

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

Installation of the current unstable version from R-Universe CRAN-like
repository (synchronised with GitHub):

```{r, eval=FALSE}
install.packages('photobiologySensors', 
                 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 sources:

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

Installation from GitHub sources does not automatically install dependencies.
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, also from R-Universe):

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

## Documentation

HTML documentation is available at
(), including the *User
Guide*.

News on updates to the different packages of the 'r4photobiology' suite are
regularly posted at ().

Two articles introduce the basic ideas behind the design of the suite and
describe its use: Aphalo P. J. (2015)
() and Aphalo P. J. (2016)
().

A book is under preparation, and the draft is currently available at
().

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
().

## Contributing

Pull requests, bug reports, and feature requests are welcome at
().

## Citation

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

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

## License

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

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