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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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.