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 used with spectrometers. It complements other packages in the suite of R packages for photobiology ‘r4photobiology’. This package contains only data.
In the update to version 0.5.0 several members of the collection of filter 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.
How many spectra are included in the current version of ‘photobiologyFilters’?
What are the names of available spectra? We use head() to limit the output.
# list names of the first 10 filters
head(names(sensors.mspct), 10)
#> [1] "Berger_UV_Biometer" "DeltaT_BF5" "flat_e"
#> [4] "flat_q" "KIPP_CUV_5" "KIPP_PQS1"
#> [7] "KIPP_UVS_A" "KIPP_UVS_B" "KIPP_UVS_E"
#> [10] "LICOR_LI_190"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.
We can use the vector to extract all these spectra as a collection.
sensors.mspct[licor_sensors]
#> $LICOR_LI_190
#> Object: response_spct [755 x 2]
#> Wavelength range 365.614 to 742.99 nm, step 0.5004987 nm
#> Time unit 1s
#>
#> # A tibble: 755 x 2
#> w.length s.q.response
#> <dbl> <dbl>
#> 1 366. 0.00181
#> 2 366. 0.00188
#> 3 367. 0.00195
#> 4 367. 0.00202
#> 5 368. 0.00209
#> 6 368. 0.00217
#> 7 369. 0.00224
#> 8 369. 0.00231
#> 9 370. 0.00238
#> 10 370. 0.00245
#> # ... with 745 more rows
#>
#> $LICOR_LI_200
#> Object: response_spct [64 x 2]
#> Wavelength range 376.154 to 1106.97 nm, step 2.68 to 51.052 nm
#> Time unit 1s
#>
#> # A tibble: 64 x 2
#> w.length s.e.response
#> <dbl> <dbl>
#> 1 376. 0.0272
#> 2 382. 0.0543
#> 3 392. 0.0788
#> 4 395. 0.106
#> 5 400. 0.133
#> 6 406. 0.160
#> 7 414. 0.185
#> 8 425. 0.209
#> 9 435. 0.234
#> 10 451. 0.255
#> # ... with 54 more rows
#>
#> $LICOR_LI_210
#> Object: response_spct [78 x 2]
#> Wavelength range 382.387 to 715.931 nm, step 1.683 to 10.516 nm
#> Time unit 1s
#>
#> # A tibble: 78 x 2
#> w.length s.e.response
#> <dbl> <dbl>
#> 1 382. 0.00335
#> 2 387. 0.00670
#> 3 390. 0.00838
#> 4 395. 0.0101
#> 5 403. 0.0101
#> 6 411. 0.0117
#> 7 414. 0.0117
#> 8 417. 0.0134
#> 9 420. 0.0151
#> 10 424. 0.0168
#> # ... with 68 more rowsPlease, see the User Guide or help pages for the names of other vectors of names for materials, suppliers, and regions 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 given by wavelengths in nanometres.
q_response(sensors.mspct[["LICOR_LI_190"]],
waveband(c(500,600)))
#> R[/q]_range.500.600
#> 98.91598
#> attr(,"time.unit")
#> [1] "second"
#> attr(,"radiation.unit")
#> [1] "total 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.
Installation of the most recent stable version from CRAN:
Installation of the current unstable version from Bitbucket:
HTML documentation is available at (https://docs.r4photobiology.info/photobiologyFilters/), 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).
Pull requests, bug reports, and feature requests are welcome at (https://bitbucket.org/aphalo/photobiologysensors).
If you use this package to produce scientific or commercial publications, please cite according to:
citation("photobiologySensors")
#>
#> To cite package 'photobiologySensors' in publications, please 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},
#> }© 2012-2020 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.