Package ‘photobiologyLEDs’ complements other
packages in the R for
photobiology suite. It contains spectral emission data for
diverse types of light emitting diodes (LEDs) and LED arrays
(leds.mspct) available as electronic components. Spectra
for LED-based lamps and other lamps are included in package ‘photobioloyLamps’.
Package ‘photobiologyLEDs’ also includes spectra from a COB LED when
dimmed using the constant current approach
(COB_dimming.mspct) and for a COB LED combined with
reflectors with different beam angles
(COB_reflectors.mspct).
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. Spectra can be easily plotted with functions and methods from
package ‘ggspectra’. The
spectra can be used seamlessly with functions from package ‘photobioloy’.
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.
library(ggspectra)
library(photobiologyLEDs)How many spectra are included in the current version of ‘photobiologyLEDs’?
length(leds.mspct)
#> [1] 93length(COB_dimming.mspct)
#> [1] 8length(COB_reflectors.mspct)
#> [1] 4What are the names of available spectra. We use head()
to limit the output.
# list names of the first 10 LEDs
head(names(leds.mspct), 10)
#> [1] "Agilent_HLMB_CB30" "Agilent_HLMB_CD31"
#> [3] "Agilent_HLMP_CB31" "Agilent_HLMP_CM30"
#> [5] "Agilent_HLMP_CM31" "Agilent_HLMP_DJ32"
#> [7] "Agilent_HLMP_DL32" "Bridgelux_3W_455nm"
#> [9] "Bridgelux_BXRE_50S2001_c_73" "CREE_XPE_480nm"To subset based on different criteria we can use predefined character
vectors of LED names. For example, vector nichia_leds lists
the names of the spectra for LEDs made by NIchia.
Nichia_leds
#> [1] "Nichia_NVSU233B_U365" "Nichia_NVSU119C_U385"
#> [3] "Nichia_NFSW757G_Rsp0a" "Nichia_NFSL757GT_Rsp0a"
#> [5] "Nichia_NFCWL036B_V3_Rfcb0" "Nichia_NF2W757GT_F1_sm505_Rfc00"
#> [7] "Nichia_unknown_757" "Nichia_NS6L183AT_H1_sw"
#> [9] "Nichia_NFSW757G_V3_Rs060"We can use the vector to extract all these spectra as a collection.
leds.mspct[Nichia_leds]
#> Object: source_mspct [9 x 1]
#> --- Member: Nichia_NVSU233B_U365 ---
#> Object: source_spct [1,313 x 2]
#> Wavelength range 251.29-900 nm, step 1.023182e-12-7.53 nm
#> Label: LED type NVSU233B_U365 from Nichia
#> Measured on 2021-10-09 22:35:17.181825 UTC
#> Time unit 1s
#> Spectral data normalized to s.e.irrad = 1 at 366.03 nm (max in 251.29-900 nm)
#>
#> # A tibble: 1,313 × 2
#> w.length s.e.irrad
#> <dbl> <dbl>
#> 1 251. 0
#> 2 256. 0
#> 3 257. 0
#> 4 257. 0
#> 5 257. 0
#> 6 258. 0
#> 7 258. 0
#> 8 259. 0
#> 9 259. 0
#> 10 260. 0
#> # ℹ 1,303 more rows
#> --- Member: Nichia_NVSU119C_U385 ---
#> Object: source_spct [1,269 x 2]
#> Wavelength range 251.29-900 nm, step 1.023182e-12-7.52 nm
#> Label: LED type NVSU119C_U385 from Nichia
#> Measured on 2021-10-09 22:29:03.495034 UTC
#> Time unit 1s
#> Spectral data normalized to s.e.irrad = 1 at 385.25 nm (max in 251.29-900 nm)
#>
#> # A tibble: 1,269 × 2
#> w.length s.e.irrad
#> <dbl> <dbl>
#> 1 251. 0
#> 2 254. 0
#> 3 254. 0
#> 4 256. 0
#> 5 257. 0
#> 6 257. 0
#> 7 257. 0
#> 8 258. 0
#> 9 258. 0
#> 10 259. 0
#> # ℹ 1,259 more rows
#> --- Member: Nichia_NFSW757G_Rsp0a ---
#> Object: source_spct [568 x 2]
#> Wavelength range 251.16-900 nm, step 1.023182e-12-7.59 nm
#> Label: LED type NFSW757G_Rsp0a from Nichia
#> Measured on 2019-06-25 14:03:10.946064 UTC
#> Time unit 1s
#> Spectral data normalized to s.e.irrad = 1 at 451.3 nm (max in 251.16-900 nm)
#>
#> # A tibble: 568 × 2
#> w.length s.e.irrad
#> <dbl> <dbl>
#> 1 251. 0
#> 2 259. 0
#> 3 260. 0
#> 4 261. 0
#> 5 261. 0
#> 6 263. 0
#> 7 263. 0
#> 8 263. 0
#> 9 264. 0
#> 10 266. 0
#> # ℹ 558 more rows
#> --- Member: Nichia_NFSL757GT_Rsp0a ---
#> Object: source_spct [645 x 2]
#> Wavelength range 251.16-900 nm, step 1.023182e-12-7.59 nm
#> Label: LED type NFSL757GT_Rsp0a from Nichia
#> Measured on 2019-06-25 14:07:51.674266 UTC
#> Time unit 1s
#> Spectral data normalized to s.e.irrad = 1 at 622.27 nm (max in 251.16-900 nm)
#>
#> # A tibble: 645 × 2
#> w.length s.e.irrad
#> <dbl> <dbl>
#> 1 251. 0
#> 2 252. 0
#> 3 252. 0
#> 4 253. 0
#> 5 253. 0
#> 6 255. 0
#> 7 258. 0
#> 8 258. 0
#> 9 259. 0
#> 10 266. 0
#> # ℹ 635 more rows
#> --- Member: Nichia_NFCWL036B_V3_Rfcb0 ---
#> Object: source_spct [796 x 2]
#> Wavelength range 251.29-900 nm, step 1.023182e-12-7.55 nm
#> Label: LED type NFCWL036B_V3_Rfcb0 from Nichia
#> Measured on 2021-10-09 20:43:51.476858 UTC
#> Time unit 1s
#> Spectral data normalized to s.e.irrad = 1 at 458.44 nm (max in 251.29-900 nm)
#>
#> # A tibble: 796 × 2
#> w.length s.e.irrad
#> <dbl> <dbl>
#> 1 251. 0
#> 2 254. 0
#> 3 254. 0
#> 4 256. 0
#> 5 257. 0
#> 6 259. 0
#> 7 259. 0
#> 8 260. 0
#> 9 260. 0
#> 10 261. 0
#> # ℹ 786 more rows
#> --- Member: Nichia_NF2W757GT_F1_sm505_Rfc00 ---
#> Object: source_spct [729 x 2]
#> Wavelength range 251.16-900 nm, step 1.023182e-12-7.59 nm
#> Label: LED type NF2W757GT_F1_sm505_Rfc00 from Nichia
#> Measured on 2019-06-25 14:22:46.214559 UTC
#> Time unit 1s
#> Spectral data normalized to s.e.irrad = 1 at 419.18 nm (max in 251.16-900 nm)
#>
#> # A tibble: 729 × 2
#> w.length s.e.irrad
#> <dbl> <dbl>
#> 1 251. 0
#> 2 252. 0
#> 3 253. 0
#> 4 254. 0
#> 5 254 0
#> 6 259. 0
#> 7 266. 0
#> 8 271. 0
#> 9 272. 0
#> 10 274. 0
#> # ℹ 719 more rows
#> --- Member: Nichia_unknown_757 ---
#> Object: source_spct [526 x 3]
#> Wavelength range 250.14-900 nm, step 1.023182e-12-7.59 nm
#> Label: LED type unknown_757 from Nichia
#> Measured on 2016-09-14 16:19:00 UTC
#> Time unit 1s
#> Spectral data normalized to s.e.irrad = 1 at 454.48 nm (max in 250.14-900 nm)
#>
#> # A tibble: 526 × 3
#> w.length s.e.irrad s.e.irrad.good
#> <dbl> <dbl> <dbl>
#> 1 250. 0 0
#> 2 251. 0 0
#> 3 252. 0 0
#> 4 258. 0 0
#> 5 265. 0 0
#> 6 273. 0 0
#> 7 281. 0 0
#> 8 288. 0 0
#> 9 296. 0 0
#> 10 303. 0 0
#> # ℹ 516 more rows
#> --- Member: Nichia_NS6L183AT_H1_sw ---
#> Object: source_spct [904 x 2]
#> Wavelength range 251.29-900 nm, step 1.023182e-12-7.48 nm
#> Label: LED type NS6L183AT_H1_sw from Nichia
#> Measured on 2021-10-09 20:15:17.948579 UTC
#> Time unit 1s
#> Spectral data normalized to s.e.irrad = 1 at 620.12 nm (max in 251.29-900 nm)
#>
#> # A tibble: 904 × 2
#> w.length s.e.irrad
#> <dbl> <dbl>
#> 1 251. 0
#> 2 256. 0
#> 3 257. 0
#> 4 257. 0
#> 5 257. 0
#> 6 258. 0
#> 7 258. 0
#> 8 259. 0
#> 9 259. 0
#> 10 260. 0
#> # ℹ 894 more rows
#> --- Member: Nichia_NFSW757G_V3_Rs060 ---
#> Object: source_spct [187 x 2]
#> Wavelength range 350-799.30696 nm, step 1-16 nm
#> Time unit 1s
#> Spectral data normalized to s.e.irrad = 1 at 450 nm (max in 350-799.31 nm)
#>
#> # A tibble: 187 × 2
#> w.length s.e.irrad
#> <dbl> <dbl>
#> 1 350 0
#> 2 366 0.000254
#> 3 369 0
#> 4 370 0
#> 5 371 0
#> 6 372 0
#> 7 373 0
#> 8 374 0
#> 9 375 0
#> 10 376 0
#> # ℹ 177 more rows
#>
#> --- END ---The package includes a character vector with the names of LED brands and LED colors as used for indexing vectors.
led_colors
#> [1] "uv" "purle" "blue" "green" "yellow" "orange" "red" "ir"led_brands
#> [1] "Agilent" "Bridgelux" "CREE" "Epileds"
#> [5] "Epistar" "HueyJann" "LCFOCUS" "LedEngin"
#> [9] "Ledguhon" "Luminus" "Marktech" "Nichia"
#> [13] "Norlux" "Osram" "QuantumDevices" "Roithner"
#> [17] "Samsung" "SeoulSemicon" "TaoYuan" "Weili"led_uses
#> [1] "plant_grow" "high_CRI"Vectors like Nichia_leds shown above are available for
all the brands listed in led_brands, all the colors in
led_colors, and all the uses in led_uses.
Summary calculations can be easily done with methods from package
‘photobiology’. Here we calculate photon irradiance. As the spectra are
normalised we pass allow.scaled = TRUE,
q_irrad(leds.mspct[["Nichia_NS6L183AT_H1_sw"]],
allow.scaled = TRUE, scale.factor = 1e6)
#> Q_Total
#> 151086898
#> attr(,"time.unit")
#> [1] "second"
#> attr(,"radiation.unit")
#> [1] "total photon irradiance"The autoplot() methods from package ‘ggspectra’ can be
used for plotting one or more spectra at a time.
autoplot(leds.mspct[["Nichia_NS6L183AT_H1_sw"]]) + 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 of the most recent stable version from CRAN:
install.packages("photobiologyLEDs")Installation of the current unstable version from GitHub:
# install.packages("devtools")
remotes::install_github("aphalo/photobiologyLEDs")HTML documentation is available at (https://docs.r4photobiology.info/photobiologyLEDs/), 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://github.com/aphalo/photobiologyLEDs).
If you use this package to produce scientific or commercial publications, please cite according to:
citation("photobiologyLEDs")
#> To cite package ‘photobiologyLEDs’ 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},
#> }© 2012-2023 Pedro J. Aphalo (pedro.aphalo@helsinki.fi). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.