photobiologyLamps

https://github.com/aphalo/photobiologylamps

Repository

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-"
)
```

# photobiologyLamps 


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Package '**photobiologyLamps**' complements other packages in the [_R for photobiology_ suite](https://www.r4photobiology.info/). It contains spectral emission data for LED, fluorescent, incandescent and other lamps (`lamps.mspct`). Spectra for light emitting diodes (LEDs) and LED arrays (`leds.mspct`) available as electronic components are included in package ['photobioloyLEDs'](https://docs.r4photobiology.info/photobiologyLEDs/). Package '**photobiologyLamps**' also includes spectra from UV-B fluorescent tubes operating at different temperatures (`qp_uvb313_temp.mspct` and `qp_uvb313_temp.spct`) and for a four-channel LED bulb supporting channel mixing (`ledsavers.mspct`).

The data are for the most part original but also include some spectra digitized from plots in manufacturers' specifications. Data have been acquired over many years, although when possible lamps have been measured again after we got a spectrometer with improved wavelength resolution. It is important for users to be aware that depending on the optical wavelength resolution of the instruments used spectra can look quite different because of the broadening of peaks. This is most obvious in lamps with narrow emission peaks like mercury vapours lamps. If you make use of the data, please inspect the metadata and read the documentation. The metadata is in most cases fairly complete, although the distance from lamps to the entrance optics is frequently unknown. For this reason spectra have been normalized. The multiplier used for normalization is part of the metadata, making it possible to recover the original spectrum. The metadata includes, when available, a descriptor of the spectrometer and the settings used for acqiring the spectral data.

This package contains only data. Data are stored as collections of spectra of class `source_mspct` from package 'photobiology', which is the core of the 
[_R for photobiology_ suite](https://www.r4photobiology.info/). Spectra can
be easily plotted with functions and methods from package ['ggspectra'](https://docs.r4photobiology.info/ggspectra/). The spectra can be used seamlesly with functions from package ['photobiology'](https://docs.r4photobiology.info/photobiology/). However,
class `source_mspct` is derived from `list` and class `source_spct` is derived from `data.frame` making the data also usable as is with base R functions.

## Examples

```{r example0, message=FALSE}
library(ggspectra)
library(photobiologyLamps)
theme_set(theme_bw())
```

The package includes spectral data for several lamps.

```{r}
length(lamps.mspct)
```

The members of the collections are named, and several vectors of names are available indexing `lamps.mspct`, such as by manufacturer,

```{r}
Philips_lamps
```

or type of lamp.

```{r}
incandescent_lamps
```

Response to temperature of UV-B fluorescent tubes.

```{r}
what_measured(qp_uvb313_temp.mspct)
```

Different settings of a four-channel LED bulb, with its own indexing vectors of member names.

```{r}
what_measured(ledsavers.mspct)
```

Different small video/photography LED lamps: `sunwayfoto_fl96.mspct`,
`elgato_klm_cct.mspct`, `elgato_klm_dim.mspct`, `amaran_m9.mspct` and
`andoer_ir49.mspct`. Each of these collections of spectra contains data
for one lamp with different dimming and/or colour temperature settings.

The first example below shows you how to plot the emission spectrum of one of the
lamps.

```{r example1, message=FALSE}
autoplot(lamps.mspct$Airam.CF.Spiraali.14W.3000K, geom = "spct",
         annotations = c("+", "title:what"))
```

The second example shows how to access metadata.

```{r example2}
what_measured(lamps.mspct$Airam.CF.Spiraali.14W.3000K)
```

## Installation

Installation of the most recent stable version from CRAN:

```{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('photobiologyLamps', 
                 repos = c('https://aphalo.r-universe.dev', 
                           'https://cloud.r-project.org'))
```

Installation of the current unstable version from GitHub:

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

## Documentation 

HTML documentation is available at (https://docs.r4photobiology.info/photobiologyLamps/), 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., Bjrn, 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/photobiologyLamps).

## Citation

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

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

## License

 2013-2024 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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