photobiologySun

https://github.com/aphalo/photobiologysun

Repository

README.Rmd

---
output:
  github_document
---

# photobiologySun 


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Package '**photobiologySun**' complements other packages in the [_R for photobiology_ suite](https://www.r4photobiology.info/). It contains spectral irradiance and irradiance data for daylight, including sunlight and shade light. Package 'photobiologySun' also includes spectra measured or simulated for different times of the day, sun elevation angles, atmospheric ozone column and ANSI and other reference spectra for solar radiation.

This package contains only data and documentation. 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 seamlessly with functions from package ['photobioloy'](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 readme-01, echo = FALSE}
knitr::opts_chunk$set(
  fig.asp = 2/3,
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
```

```{r example-02, message=FALSE}
library(ggspectra)
library(photobiologySun)
```

How many spectra are contained in the collection of spectra `gap.mspct`? In this case the spectra are from a fast time series of measurements.

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

What are their names?

```{r example-03a}
names(gap.mspct)
```

How many spectra are contained in the collection of spectra `sun_reference.mspct`?

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

What are their names? (The three "AM0" spectra are for the extraterrestrial solar spectrum, AM0 = zero atmosphera. ASTM G173 corresponds to AM1.5 and frequently used in engineering.)

```{r example-04}
names(sun_reference.mspct)
```

Summary calculations can be easily done with methods from package 'photobiology'. Here we calculate photon irradiance with function `q_irrad()` for another collection of spectra. As the spectra are normalised we pass `allow.scaled = TRUE`, 

```{r example-06}
q_irrad(sun_hourly_august.spct, scale.factor = 1e6) # Q_Total: umol m-2 s-1
```

The `autoplot()` methods from package 'ggspectra' can be used for plotting one or more spectra at a time.

```{r}
autoplot(gap.mspct[1:10], annotations = c("-", "peaks")) + 
  theme_bw()
```

The classes of the objects used to store the spectral data are derived from `"data.frame"` making direct use of the data with functions and methods from base R and various packages easy.

## Installation

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

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

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("devtools")
devtools::install_github("aphalo/photobiologySun")
```

## Documentation 

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

## Citation

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

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

## License

© 2012-2024 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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