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Introduction

This package, is a data only package, part of a suite, which has package ‘photobiology’ at its core. Please visit (https://www.r4photobiology.info/) for more details. For more details on plotting spectra, please consult the documentation for package ‘ggspectra’, and for information on the calculation of summaries and maths operations between spectra, please, consult the documentation for package ‘photobiology’.

In this brief User Guide we describe how to re-scale the normalized spectra, and how to access individual spectra or subsets of spectra.

Spectra in the package are contained in three collections: lamps.mspct contains spectral data for various types of lamps emiiting a fixed color of light; ledsavers.mspct contains spectral data for a LED bulb with four color channels allowing it to output 16 different colors of light; qp_uvb313_temp.mspct contains spectral data for UV lamps under seven different temperatures. In addition qp_uvb313_temp.spct contains the same data in a single spectral object.

In addtion to the objects containing the data itself, several character vectors of names of spectra are provide to facilitate the retrieval of subsets of spectra.

Accessing individual spectra

The source_spct member objects in lamps.mspct can be accessed through their names or through a numeric index. As the numeric indexes are likely to change with updates to the package, their use is discouraged. Names as character strings should be used instead. The names are listed in the documentation and also available through the “Data Catalogue” vignette. They can also be listed with method names().

names(lamps.mspct)
##  [1] "Airam.CF.15W.2700K"                  
##  [2] "Airam.CF.Spiraali.14W.3000K"         
##  [3] "Airam.LED.11W.4000K"                 
##  [4] "Airam.LED.14W.4000K"                 
##  [5] "Airam.LED.9W.3000K"                  
##  [6] "Amaran.M9.LED.video.light.5500K"     
##  [7] "Convoy.2plus.LED.UVA.flashlight"     
##  [8] "Fluence.LED.AnthoSpec"               
##  [9] "Fluence.LED.PhysioSpec.BROAD"        
## [10] "Fluence.LED.PhysioSpec.BROAD.R3"     
## [11] "Fluence.LED.PhysioSpec.BROAD.R6"     
## [12] "Fluence.LED.PhysioSpec.BROAD.R9B"    
## [13] "Fluence.LED.PhysioSpec.Greenhouse"   
## [14] "Fluence.LED.PhysioSpec.Indoor"       
## [15] "Generic.germicidal"                  
## [16] "Generic.Inc.bulb.60W"                
## [17] "Generic.LED.9W.mosquito"             
## [18] "Generic.LED.NIR.flashlight"          
## [19] "Generic.LED.UVA.flashlight"          
## [20] "Godox.XeF.AD200.H200.flash"          
## [21] "Godox.XeF.AD200.H200j.ADFT200.flash" 
## [22] "Godox.XeF.AD200.H200j.FTSTS40w.flash"
## [23] "Godox.XeF.AD200.H200R.flash"         
## [24] "Ikea.LED.6.3W.2700K"                 
## [25] "Jaxman.U1c.LED.UVA.flood.flashlight" 
## [26] "LCDlighting.FT.UVA.BL"               
## [27] "Ledenergie.LED.Nano.T8.9.5W.4000K"   
## [28] "Ledenergie.LED.Teho.T8.9W.4000K"     
## [29] "Ledstore.LED.10W.4000K"              
## [30] "Osram.FT.36W.25"                     
## [31] "Osram.FT.L36W.840"                   
## [32] "Osram.HPS.Super.Vialox"              
## [33] "Osram.Inc.20W"                       
## [34] "Osram.LED.10W.2700K"                 
## [35] "Osram.LED.8W.2700K"                  
## [36] "Osram.MH.HQIT.400W"                  
## [37] "Philips.CF.PLS.11W.927"              
## [38] "Philips.FT.TL.40W.01.uv"             
## [39] "Philips.FT.TL.40W.12"                
## [40] "Philips.FT.TL.40W.12.uv"             
## [41] "Philips.FT.TL5.35W.830.HE"           
## [42] "Philips.FT.TLD.36W.15"               
## [43] "Philips.FT.TLD.36W.18"               
## [44] "Philips.FT.TLD.36W.18.lores"         
## [45] "Philips.FT.TLD.36W.83"               
## [46] "Philips.FT.TLD.36W.89"               
## [47] "Philips.FT.TLD.36W.92"               
## [48] "Philips.FT.TLD.36W.965"              
## [49] "Philips.FT.TLD.36W.BLB.108"          
## [50] "Philips.FT.TLL.36W.950"              
## [51] "Philips.Inc.50W.spot.halogen"        
## [52] "Philips.LED.T8.10W.840"              
## [53] "QPanel.FT.UVB313.40W"                
## [54] "QPanel.FT.UVB340.40W"                
## [55] "Sunwayfoto.LED.FL96.at.3000K"        
## [56] "Sunwayfoto.LED.FL96.at.4000K"        
## [57] "Sunwayfoto.LED.FL96.at.5500K"        
## [58] "Sylvania.FT.215W.VHO"                
## [59] "Toshiba.LED.12W.2700K"               
## [60] "Toshiba.LED.9.5W.2700K"              
## [61] "V.light.LED.2W.6000K"                
## [62] "Valoya.LED.B50.AP67.LED.grow.lamp"

We can use a name as index to extract an individual source_spct object.

lamps.mspct$Generic.Inc.bulb.60W
## Object: source_spct [601 x 2]
## Wavelength range 300-900 nm, step 1 nm 
## Label: Incandescent lamp: Generic bulb 60W ca. 1995 
## Measured on 0-08-18 13:47:11 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 900 nm (max in 300-900 nm)
## 
## # A tibble: 601 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1      300  0.000665
##  2      301  0.000325
##  3      302  0.000956
##  4      303  0.000702
##  5      304  0.000306
##  6      305  0.000825
##  7      306  0.00103 
##  8      307  0.000361
##  9      308  0.000497
## 10      309  0.000627
## # ℹ 591 more rows

Or a character string.

lamps.mspct[["Generic.Inc.bulb.60W"]]
## Object: source_spct [601 x 2]
## Wavelength range 300-900 nm, step 1 nm 
## Label: Incandescent lamp: Generic bulb 60W ca. 1995 
## Measured on 0-08-18 13:47:11 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 900 nm (max in 300-900 nm)
## 
## # A tibble: 601 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1      300  0.000665
##  2      301  0.000325
##  3      302  0.000956
##  4      303  0.000702
##  5      304  0.000306
##  6      305  0.000825
##  7      306  0.00103 
##  8      307  0.000361
##  9      308  0.000497
## 10      309  0.000627
## # ℹ 591 more rows

Be aware that according to R’s rules, using single square brackets will return a source_mspct object possibly of length one. This statement is not equivalent to the one in the chunk immediately above.

lamps.mspct["Generic.Inc.bulb.60W"]
## Object: source_mspct [1 x 1]
## --- Member: Generic.Inc.bulb.60W ---
## Object: source_spct [601 x 2]
## Wavelength range 300-900 nm, step 1 nm 
## Label: Incandescent lamp: Generic bulb 60W ca. 1995 
## Measured on 0-08-18 13:47:11 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 900 nm (max in 300-900 nm)
## 
## # A tibble: 601 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1      300  0.000665
##  2      301  0.000325
##  3      302  0.000956
##  4      303  0.000702
##  5      304  0.000306
##  6      305  0.000825
##  7      306  0.00103 
##  8      307  0.000361
##  9      308  0.000497
## 10      309  0.000627
## # ℹ 591 more rows
## 
## --- END ---

Accessing subsets of spectra

We can subset the source_mspct object by indexing with vectors of character strings. The package provides some predefined ones, and users can easily define their own, either as constants or through computation. Here we use a vector defined by the package.

lamps.mspct[Toshiba_lamps]
## Object: source_mspct [2 x 1]
## --- Member: Toshiba.LED.12W.2700K ---
## Object: source_spct [591 x 2]
## Wavelength range 251.16-898.81 nm, step 1.023182e-12-7.56 nm 
## Label: LED lamp:  Toshiba 12W 2700K 
## Measured on 2018-02-12 09:08:23.957523 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 607.26 nm (max in 251.16-898.81 nm)
## 
## # A tibble: 591 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1     251.         0
##  2     256.         0
##  3     256.         0
##  4     257.         0
##  5     257.         0
##  6     258.         0
##  7     258.         0
##  8     259.         0
##  9     259.         0
## 10     260.         0
## # ℹ 581 more rows
## --- Member: Toshiba.LED.9.5W.2700K ---
## Object: source_spct [678 x 2]
## Wavelength range 251.29-898.97 nm, step 1.023182e-12-7.55 nm 
## Label: LED lamp:  Toshiba 9.5W 2700K 
## Measured on 2021-09-02 19:48:00.171366 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 605.57 nm (max in 251.29-898.97 nm)
## 
## # A tibble: 678 × 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 668 more rows
## 
## --- END ---

And below we use a computed one. In this case we extract the member spectra with names containing the string “toshiba”. More generaly one can search for matching names within the collection of spectra.

lamps.mspct[grep("Toshiba", names(lamps.mspct))]
## Object: source_mspct [2 x 1]
## --- Member: Toshiba.LED.12W.2700K ---
## Object: source_spct [591 x 2]
## Wavelength range 251.16-898.81 nm, step 1.023182e-12-7.56 nm 
## Label: LED lamp:  Toshiba 12W 2700K 
## Measured on 2018-02-12 09:08:23.957523 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 607.26 nm (max in 251.16-898.81 nm)
## 
## # A tibble: 591 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1     251.         0
##  2     256.         0
##  3     256.         0
##  4     257.         0
##  5     257.         0
##  6     258.         0
##  7     258.         0
##  8     259.         0
##  9     259.         0
## 10     260.         0
## # ℹ 581 more rows
## --- Member: Toshiba.LED.9.5W.2700K ---
## Object: source_spct [678 x 2]
## Wavelength range 251.29-898.97 nm, step 1.023182e-12-7.55 nm 
## Label: LED lamp:  Toshiba 9.5W 2700K 
## Measured on 2021-09-02 19:48:00.171366 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 605.57 nm (max in 251.29-898.97 nm)
## 
## # A tibble: 678 × 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 668 more rows
## 
## --- END ---

Set algebra operations can be used with the indexing vectors as each vector describes a single property: color, brand, type, etc.

lamps.mspct[intersect(Philips_lamps, red_lamps)]
## Object: source_mspct [6 x 1]
## --- Member: Philips.CF.PLS.11W.927 ---
## Object: source_spct [301 x 2]
## Wavelength range 300-900 nm, step 2 nm 
## Label: Compact fluorescent lamp: Philips PLS 11W 927 ca. 1995 
## Measured on 0-10-18 08:51:11 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 612 nm (max in 300-900 nm)
## 
## # A tibble: 301 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1      300  0.000135
##  2      302  0.000370
##  3      304  0.000351
##  4      306  0.000227
##  5      308  0.00240 
##  6      310  0.00804 
##  7      312  0.0151  
##  8      314  0.0171  
##  9      316  0.0115  
## 10      318  0.00536 
## # ℹ 291 more rows
## --- Member: Philips.FT.TL5.35W.830.HE ---
## Object: source_spct [1,101 x 2]
## Wavelength range 251.16-898.81 nm, step 0.43-4.92 nm 
## Label: Fluorescent tube: Philips FT TL5 35W 830 HE 
## Measured on 2018-02-12 09:57:35.344863 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 611.35 nm (max in 251.16-898.81 nm)
## 
## # A tibble: 1,101 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1     251.   0.00739
##  2     252.   0      
##  3     252.   0      
##  4     253.   0      
##  5     253.   0.00279
##  6     254.   0.00305
##  7     254    0      
##  8     254.   0      
##  9     255.   0.00237
## 10     255.   0.00765
## # ℹ 1,091 more rows
## --- Member: Philips.FT.TLD.36W.15 ---
## Object: source_spct [601 x 2]
## Wavelength range 300-900 nm, step 1 nm 
## Label: Fluorescent tube: Philips TLD 36W 15 ca. 1995 
## Measured on 0-08-23 10:16:11 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 660 nm (max in 300-900 nm)
## 
## # A tibble: 601 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1      300  0.000196
##  2      301  0.000959
##  3      302  0.000752
##  4      303  0.00110 
##  5      304  0.00126 
##  6      305  0.000885
##  7      306  0.000521
##  8      307  0.00153 
##  9      308  0.000167
## 10      309  0.000493
## # ℹ 591 more rows
## --- Member: Philips.FT.TLD.36W.83 ---
## Object: source_spct [601 x 2]
## Wavelength range 300-900 nm, step 1 nm 
## Label: Fluorescent tube: Philips TLD 36W 83 ca. 1995 
## Measured on 0-08-23 11:51:11 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 613 nm (max in 300-900 nm)
## 
## # A tibble: 601 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1      300  0.000381
##  2      301  0.000497
##  3      302  0.000426
##  4      303  0.000476
##  5      304  0.000467
##  6      305  0.000343
##  7      306  0.000449
##  8      307  0.000606
##  9      308  0.00130 
## 10      309  0.00229 
## # ℹ 591 more rows
## --- Member: Philips.FT.TLD.36W.89 ---
## Object: source_spct [601 x 2]
## Wavelength range 300-900 nm, step 1 nm 
## Label: Fluorescent tube: Philips TLD 36W 89 ca. 1995 
## Measured on 0-08-23 15:19:11 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 613 nm (max in 300-900 nm)
## 
## # A tibble: 601 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1      300  0.000477
##  2      301  0.000560
##  3      302  0.00100 
##  4      303  0.000626
##  5      304  0.000965
##  6      305  0.000860
##  7      306  0.000760
##  8      307  0.000746
##  9      308  0.00114 
## 10      309  0.00176 
## # ℹ 591 more rows
## --- Member: Philips.FT.TLL.36W.950 ---
## Object: source_spct [601 x 2]
## Wavelength range 300-900 nm, step 1 nm 
## Label: Fluorescent tube: Philips TLL 36W 950 ca. 1995 
## Measured on 0-08-23 08:44:11 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 613 nm (max in 300-900 nm)
## 
## # A tibble: 601 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1      300 0.0000697
##  2      301 0.0000682
##  3      302 0.0000382
##  4      303 0.0000561
##  5      304 0.0000733
##  6      305 0.0000359
##  7      306 0.0000353
##  8      307 0.0000346
##  9      308 0.000136 
## 10      309 0.000250 
## # ℹ 591 more rows
## 
## --- END ---

Rescaling spectral data

The spectra are normalized, and consequently, several summaries expressed in absolute units are undefined, and trigger errors. Summaries like ratios which are not affected by normalization are allowed and valid. The data have been normalized as the measuring conditions used are not all the same, and in many cases not well characterized (e.g. distance to light source, or exact alignment of the spectrometer input optics with respect to the center of the light beam from sources).

These uncertainties in the measurment conditions are likely to have minimal effect on the shape of the spectrum when plotted. This allows us to reconstruct the spectrum at a different distance from the lamp(s) or under a different number of lamps as long as we know the irradiance for some known waveband, such as PAR.

In this section we will rescale the spectral data so that after re-scaling a given target value for a summary quantity will be true. As an example, we will rescale one spectrum so that it yields an energy irradiance of 100 W m-2 for the range 400 to 700 nm. By default the returned spectrum is not labelled as being expressed in relative units, as the expectation is that the operation is done to obtain spectral emission data that could have been measured at a target condition that we want to simulate or reconstruct.

my.spct <- fscale(lamps.mspct$Generic.Inc.bulb.60W,
                  range = c(400, 700),
                  f = e_irrad,
                  target = 100
                  )
e_irrad(my.spct, waveband(c(400,700)))
## E_range.400.700 
##             100 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total energy irradiance"
is_scaled(my.spct)
## [1] FALSE

To do the scaling based on photon irradiance, different approaches are available to change the default. Here as above we specify the function to use through the argument passed to f and set a suitable target in mol m-2 s-1. We use 300e-6 to indicate 300 umol m-2 s-1.

my.spct <- fscale(lamps.mspct$Generic.Inc.bulb.60W,
                  range = c(400, 700),
                  f = q_irrad,
                  target = 300e-6
                  )
q_irrad(my.spct, waveband(c(400,700)))
## Q_range.400.700 
##           3e-04 
## attr(,"time.unit")
## [1] "second"
## attr(,"radiation.unit")
## [1] "total photon irradiance"

In the special case when target == 1, the default changes, assuming that in this case the intention is to re-express the spectral data in relative units.

my.spct <- fscale(lamps.mspct$Generic.Inc.bulb.60W,
                  range = c(400, 700),
                  f = e_irrad,
                  target = 1
                  )
is_scaled(my.spct)
## [1] TRUE

If we want to override the defaults for tagging as scaled, we ccan pass a suitable argument to parameter set.scaled of fscale().

In addition to scaling based of the summary calculated by a function, as shown above, it is frequent to normalize spectral data. In this case scaling is done so that spectral irradiance matches a certain value at an specific wavelength. In most cases, the wavelength used is that of the maximal spectral irradiance, and the target value is 1. These are the defaults and in this case the returned spectra are always labeled as being normalized. We use a blue fluorescent tube for this example.

normalize(lamps.mspct$Philips.FT.TLD.36W.15)
## Object: source_spct [601 x 2]
## Wavelength range 300-900 nm, step 1 nm 
## Label: Fluorescent tube: Philips TLD 36W 15 ca. 1995 
## Measured on 0-08-23 10:16:11 UTC 
## Time unit 1s
## Spectral data normalized to s.e.irrad = 1 at 660 nm (max in 300-900 nm)
## 
## # A tibble: 601 × 2
##    w.length s.e.irrad
##       <dbl>     <dbl>
##  1      300  0.000196
##  2      301  0.000959
##  3      302  0.000752
##  4      303  0.00110 
##  5      304  0.00126 
##  6      305  0.000885
##  7      306  0.000521
##  8      307  0.00153 
##  9      308  0.000167
## 10      309  0.000493
## # ℹ 591 more rows

Ratios can be calculated directly as they are not affected by normalization or linear rescaling.

q_ratio(my.spct, Red("Smith10"), Far_red("Smith10"))
## R:FR[q:q] 
## 0.6606633 
## attr(,"radiation.unit")
## [1] "q:q ratio"

Plotting the spectra

Using autoplot() methods for spectra defined in package ‘ggspectra’ annotated plotting are created with automatically genrateda xis labels, annotations and decorations. The defaults can be easily changed, please see the documentation in package ‘ggspectra’. For most of the data included in the package, as told above, exact alignment was not ensured and the exact distance not recorded. In such cases the data included in the package have been normalized to 1 at the tallest peak of emission, as can be seen in the example below.

autoplot(lamps.mspct$Osram.LED.8W.2700K)

Data for a four channel, remote controlled, LED bulb is included in object ledsavers.mspct.

what_measured(ledsavers.mspct$purple)
## [1] "LedSavers 7.5W four channels (WRGB) LED lamp."
how_measured(ledsavers.mspct$purple)
## [1] "Array spectrometer, Ocean Optics Maya 2000 Pro; Bentham cosine diffuser D7H; distance unknown."

In this case, data are not normalized, as all spectra in the object have been measure with the lamp and entrance optics in exactly the same position, controlling emission with wireless remote controller. In the next example we see that purple is created as a mix of blue and red light.

autoplot(ledsavers.mspct$purple)

Using the ggplot() method for spectra from package ‘ggspectra’ plus geometries and statistics from package ‘ggplot2’ we gain additional control on the design.

ggplot(ledsavers.mspct$purple) +
  geom_line(linetype = "dashed") +
  theme_classic()

We can also plot multiple spectra. In this example we plot the pure emission from each of the four channels of the bulb.

autoplot(ledsavers.mspct[c( "W", "R", "G", "B")],
         annotations = c("+", "title:what")) +
  labs(linetype = "Channel")
## Warning in autotitle(object = object, object.label = object.label, time.format
## = time.format, : Multiple spectra: ignoring requested attr(s) in title.

Using the data in other contexts

In general it will be easiest to use methods from packages in the ‘r4photobiology’ suite for plotting and calculation of various summaries. However, as source_mspct is a class derived from list, and source_spct is derived from tibble::tibble that is a partly compatible reimplementation of data.frame the data can be used very easily with R functions expecting data frames as input.

head(as.data.frame(lamps.mspct$Osram.LED.8W.2700K))
##   w.length s.e.irrad
## 1   251.16         0
## 2   258.75         0
## 3   266.34         0
## 4   273.92         0
## 5   278.65         0
## 6   281.50         0

Of course attach and with also work as expected.

attach(lamps.mspct)
q_ratio(Osram.LED.8W.2700K, Blue(), Red())
## Blue:Red[q:q] 
##     0.1395062 
## attr(,"radiation.unit")
## [1] "q:q ratio"
detach(lamps.mspct)
attach(lamps.mspct)
with(Osram.LED.8W.2700K, max(w.length))
## [1] 898.81
detach(lamps.mspct)
with(lamps.mspct, q_ratio(Osram.LED.8W.2700K, Blue(), Red()))
## Blue:Red[q:q] 
##     0.1395062 
## attr(,"radiation.unit")
## [1] "q:q ratio"