README.md
In photobiologyFilters: Spectral Transmittance and Spectral Reflectance Data

photobiologyFilters

Package photobiologyFilters is a collection of spectral transmittance data for more than 300 filters measured in our lab, by collaborators or for which data have been made available by the suppliers for inclusion in this package. It also contains spectral reflectance data and spectral refraction index data for some materials and spectral reflectance data for some man-made and natural land surfaces.

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 “filters” to avoid possible name clashes with other packages and also to improve naming consistency.

library(photobiologyFilters)

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

length(filters.mspct)
#> [1] 339

length(metals.mspct)
#> [1] 12

length(materials.mspct)
#> [1] 14

length(refractive_index.mspct)
#> [1] 15

What are the names of available spectra? We use head() to limit the output.

# list names of the first 10 filters
head(names(filters.mspct), 10)
#>  [1] "Baader_U_filter"            "BPI_Luminance"             
#>  [3] "BPI_Solatrol"               "BW_007_Clear_MRC_nano"     
#>  [5] "Courtaulds_CA_115um"        "Courtaulds_CA_115um_age000"
#>  [7] "Courtaulds_CA_115um_age020" "Courtaulds_CA_115um_age030"
#>  [9] "Courtaulds_CA_115um_age060" "Courtaulds_CA_115um_age100"

To subset based on different criteria we can use predefined character vectors of filter names. For example, vector polyester lists the names of the spectra for filters made of polyester (PET).

polyester_filters
#> [1] "Foiltek_Clear_PET_G"             "McDermit_PET_Autostat_CT5_125um"

We can use the vector to extract all these spectra as a collection.

filters.mspct[polyester_filters]
#> Object: filter_mspct [2 x 1]
#> --- Member: Foiltek_Clear_PET_G ---
#> Object: filter_spct [911 x 2]
#> Wavelength range 190 to 1100 nm, step 1 nm 
#> Label: Polyethylene terephthalate (PET), 'polyester'; clear sheet; new 
#> Transmittance of type 'total'
#> Rfr (/1): 0.097, thickness (mm): 3, attenuation mode: absorption.
#> 
#> # A tibble: 911 x 2
#>    w.length      Tfr
#>       <dbl>    <dbl>
#>  1      190 0.000105
#>  2      191 0.000104
#>  3      192 0.000104
#>  4      193 0.000103
#>  5      194 0.000102
#>  6      195 0.000102
#>  7      196 0.000102
#>  8      197 0.000101
#>  9      198 0.000100
#> 10      199 0.000100
#> # ... with 901 more rows
#> --- Member: McDermit_PET_Autostat_CT5_125um ---
#> Object: filter_spct [561 x 2]
#> Wavelength range 240 to 800 nm, step 1 nm 
#> Label: Polyester, clear film, 0.000125 m thick, Autostat CT5 from McDermit Autotype; new 
#> Transmittance of type 'total'
#> Rfr (/1): 0.074, thickness (mm): 0.125, attenuation mode: absorption.
#> 
#> # A tibble: 561 x 2
#>    w.length     Tfr
#>       <int>   <dbl>
#>  1      240 0.00482
#>  2      241 0.00464
#>  3      242 0.00446
#>  4      243 0.00429
#>  5      244 0.00414
#>  6      245 0.004  
#>  7      246 0.004  
#>  8      247 0.004  
#>  9      248 0.004  
#> 10      249 0.004  
#> # ... with 551 more rows
#> 
#> --- END ---

The package includes a character vector with the names of these vectors of names that are available.

all_filter_accessors
#>  [1] "acetate_filters"            "acrylic_filters"           
#>  [3] "baader_filters"             "band_pass_filters"         
#>  [5] "blue_filters"               "blue_green_filters"        
#>  [7] "bpi_visqueen_filters"       "bw_filters"                
#>  [9] "clear_filters"              "courtaulds_filters"        
#> [11] "etola_filters"              "evonik_filters"            
#> [13] "fake_unbranded_filters"     "firecrest_filters"         
#> [15] "foiltek_filters"            "fotga_filters"             
#> [17] "green_filters"              "haida_filters"             
#> [19] "heat_filters"               "heliopan_filters"          
#> [21] "hoya_filters"               "kenko_filters"             
#> [23] "kolarivision_filters"       "lee_filters"               
#> [25] "long_pass_filters"          "mcdermit_filters"          
#> [27] "midopt_filters"             "neutral_filters"           
#> [29] "old_schott_filters"         "optical_glass_filters"     
#> [31] "orange_filters"             "photography_filters"       
#> [33] "plastic_film_filters"       "plastic_sheet_filters"     
#> [35] "plexiglas_filters"          "polycarbonate_filters"     
#> [37] "polyester_filters"          "polystyrene_filters"       
#> [39] "polyvynil_chloride_filters" "red_nir_filters"           
#> [41] "rocolax_filters"            "rosco_filters"             
#> [43] "schott_filters"             "short_pass_filters"        
#> [45] "tiffen_filters"             "uqg_filters"               
#> [47] "uv_filters"                 "uvir_cut_filters"          
#> [49] "uvroptics_filters"          "xl_horticulture_filters"   
#> [51] "yellow_filters"             "zeiss_filters"             
#> [53] "zomei_filters"

Please, 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 transmittance for two regions of the spectrum given by wavelengths in nanometres.

transmittance(filters.mspct[["Foiltek_Clear_PET_G"]], 
              list(waveband(c(250, 315)), waveband(c(500,600))))
#> Tfr(wl)_range.250.315 Tfr(wl)_range.500.600 
#>          0.0001840984          0.8759395389 
#> attr(,"Tfr.type")
#> [1] "unknown"
#> attr(,"radiation.unit")
#> [1] "transmittance average"

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:

install.packages("photobiologyFilters")

Installation of the current unstable version from Bitbucket:

# install.packages("devtools")
devtools::install_bitbucket("aphalo/photobiologyfilters")

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/photobiologyfilters).

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

citation("photobiologyFilters")
#> 
#> To cite package 'photobiologyFilters' 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},
#>   }