README

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

library(photobiologySensors)
eval_ggspectra <- requireNamespace("ggspectra", quietly = TRUE)
if (eval_ggspectra) library(ggspectra)

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

length(sensors.mspct)
#> [1] 56

# list names of the first 10 sensors
head(names(sensors.mspct), 10)
#>  [1] "ams_AS7263"          "ams_AS7331"          "ams_AS7341"         
#>  [4] "ams_AS7343"          "ams_TSL2591"         "Vishay_VEML6075"    
#>  [7] "ams_TSL254R"         "ams_TSL257"          "Analytik_Jena_UVX25"
#> [10] "Analytik_Jena_UVX31"

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.

kipp_sensors
#> [1] "KIPP_CM21"  "KIPP_CUV_5" "KIPP_PQS1"  "KIPP_UVS_A" "KIPP_UVS_B"
#> [6] "KIPP_UVS_E"

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

sensors.mspct[intersect(kipp_sensors, par_sensors)]
#> Object: response_mspct [1 x 1]
#> --- Member: KIPP_PQS1 ---
#> Object: response_spct [202 x 2]
#> Wavelength range 391.431-717.608 nm, step 0.5010399-4.00832 nm 
#> Label: KIPP PQS1 light sensor 
#> Variables:
#>  w.length: Wavelength [nm]
#>  s.e.response: Spectral energy response [W-1 m2 nm] 
#> --
#> # A tibble: 202 × 2
#>    w.length s.e.response
#>       <dbl>        <dbl>
#>  1     391.       0.0245
#>  2     392.       0.0327
#>  3     392.       0.0410
#>  4     393.       0.0561
#>  5     394.       0.0650
#>  6     394.       0.0753
#>  7     395.       0.0960
#>  8     396.       0.119 
#>  9     397.       0.134 
#> 10     397.       0.153 
#> # ℹ 192 more rows
#> 
#> --- END ---

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.

q_response(sensors.mspct[["LICOR_LI_190R"]], 
           list(waveband(c(400, 700)), waveband(c(700, 800))),
           quantity = "contribution")
#>  R/Rtot[/q]_range.400.700 R/Rtot[/q]_range.700.800[ 
#>                0.98821737                0.00870119 
#> attr(,"time.unit")
#> [1] "second"
#> attr(,"radiation.unit")
#> [1] "contribution photon response"

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.

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

install.packages("photobiologySensors")

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

install.packages('photobiologySensors', 
                 repos = c('https://aphalo.r-universe.dev', 
                           'https://cloud.r-project.org'))

# 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):

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

Documentation

News on updates to the different packages of the ‘r4photobiology’ suite are regularly posted at (https://www.r4photobiology.info/).

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

Citation

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

citation("photobiologySensors")
#> To cite package ‘photobiologySensors’ in publications 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