Methods of generic function summary for objects of spectral classes and of classes for collections of spectra.
Usage
# S3 method for class 'generic_spct'
summary(
object,
maxsum = 7,
digits = max(3, getOption("digits") - 3),
...,
expand = "none"
)
# S3 method for class 'generic_mspct'
summary(
object,
maxsum = 7,
digits = max(3, getOption("digits") - 3),
idx = "spct.idx",
which.metadata = NULL,
expand = "none",
...
)Arguments
- object
An object of one of the spectral classes for which a summary is desired.
- maxsum
integer Indicates how many levels should be shown for factors.
- digits
integer Used for number formatting with
format().- ...
additional arguments affecting the summary produced, ignored in current version.
- expand
character One of
"none","collection","each"or"auto"indicating if multiple spectra in long form should be summarized as a collection or individually.- idx
character Name of the column with the names of the members of the collection of spectra.
- which.metadata
character vector Names of attributes to retrieve, or "none" or "all". Obeyed if
expand = FALSE, its default.
Value
A summary object matching the class of object, or a list of
such objects or a summary object for a matching collection of spectra.
Metadata stored in attributes are copied to identical attributes in the
returned summary objects except when object is a collection
of spectra or if expand = "collection" is passed in the call. In
this two cases, a condensed summary is returned as a data frame and
attributes from each member can be copied to variables in it.
Details
Objects are summarized as is, ignoring the current settings of R options
photobiology.radiation.unit and photobiology.filter.qty. Unlike
R's summary, these methods can optionally summarize each spectrum stored in
long form returning a list of summaries. Although this is frequently the most
informative approach, the default remains similar to summary() method
from R: to summarize object as a whole. Alternatively, multiple
spectra stored in long form, can optionally be summarized also as a
collection of spectra. Passing "auto" in the call, is equivalent to
passing "each" or "collection" depending on the number of
spectra contained in the object.
Examples
summary(sun.spct)
#> Summary of source_spct [522 x 3] object: sun.spct
#> Wavelength range 280-800 nm, step 0.9230769-1 nm
#> Label: sunlight, simulated
#> Measured on 2010-06-22 09:51:00 UTC
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI
#> Variables:
#> w.length: Wavelength [nm]
#> s.e.irrad: Spectral energy irradiance [W m-2 nm-1]
#> s.q.irrad: Spectral photon irradiance [mol s-1 m-2 nm-1]
#> --
#> w.length s.e.irrad s.q.irrad
#> Min. :280.0 Min. :0.0000 Min. :0.000e+00
#> 1st Qu.:409.2 1st Qu.:0.4115 1st Qu.:1.980e-06
#> Median :539.5 Median :0.5799 Median :2.929e-06
#> Mean :539.5 Mean :0.5160 Mean :2.407e-06
#> 3rd Qu.:669.8 3rd Qu.:0.6664 3rd Qu.:3.155e-06
#> Max. :800.0 Max. :0.8205 Max. :3.375e-06
class(summary(sun.spct))
#> [1] "summary_source_spct" "summary_generic_spct" "list"
summary(two_filters.spct)
#> Summary of filter_spct [879 x 3] object: two_filters.spct
#> containing 2 spectra in long form
#> Wavelength range 240-800 nm, step -610-67 nm
#> spct_1 label: Polyester, clear film, 0.000125 m thick, Autostat CT5 from McDermit Autotype; new
#> spct_2 label: Theatrical 'gel', type 'Canary Supergel no312; new; from Rosco, UK
#> Variables:
#> w.length: Wavelength [nm]
#> Tfr: Total spectral transmittance [/1]
#> --
#> w.length Tfr spct.idx
#> Min. :190.0 Min. :0.00001 spct_1:454
#> 1st Qu.:359.5 1st Qu.:0.00400 spct_2:425
#> Median :492.0 Median :0.89664
#> Mean :496.6 Mean :0.58450
#> 3rd Qu.:643.5 3rd Qu.:0.91429
#> Max. :800.0 Max. :0.92543
class(summary(two_filters.spct))
#> [1] "summary_filter_spct" "summary_generic_spct" "list"
summary(sun_evening.spct)
#> Summary of source_spct [7,965 x 3] object: sun_evening.spct
#> containing 5 spectra in long form
#> Wavelength range 290-1000 nm, step 0.34-0.47 nm
#> Label: cosine.hour.9
#> time.01 measured on 2023-06-12 18:38:00.379657 UTC
#> time.02 measured on 2023-06-12 18:39:00.797266 UTC
#> time.03 measured on 2023-06-12 18:40:00.714554 UTC
#> time.04 measured on 2023-06-12 18:41:00.768459 UTC
#> time.05 measured on 2023-06-12 18:42:00.769065 UTC
#> Measured at 60.227 N, 24.018 E; Viikki, Helsinki, FI
#> Variables:
#> w.length: Wavelength [nm]
#> s.e.irrad: Spectral energy irradiance [W m-2 nm-1]
#> --
#> w.length s.e.irrad spct.idx
#> Min. : 290.0 Min. :0.00000 time.01:1593
#> 1st Qu.: 474.4 1st Qu.:0.02315 time.02:1593
#> Median : 654.8 Median :0.03892 time.03:1593
#> Mean : 651.6 Mean :0.03659 time.04:1593
#> 3rd Qu.: 830.3 3rd Qu.:0.04888 time.05:1593
#> Max. :1000.0 Max. :0.07503
summary(two_filters.spct, expand = "none")
#> Summary of filter_spct [879 x 3] object: two_filters.spct
#> containing 2 spectra in long form
#> Wavelength range 240-800 nm, step -610-67 nm
#> spct_1 label: Polyester, clear film, 0.000125 m thick, Autostat CT5 from McDermit Autotype; new
#> spct_2 label: Theatrical 'gel', type 'Canary Supergel no312; new; from Rosco, UK
#> Variables:
#> w.length: Wavelength [nm]
#> Tfr: Total spectral transmittance [/1]
#> --
#> w.length Tfr spct.idx
#> Min. :190.0 Min. :0.00001 spct_1:454
#> 1st Qu.:359.5 1st Qu.:0.00400 spct_2:425
#> Median :492.0 Median :0.89664
#> Mean :496.6 Mean :0.58450
#> 3rd Qu.:643.5 3rd Qu.:0.91429
#> Max. :800.0 Max. :0.92543
summary(two_filters.spct, expand = "each")
#> $spct_1
#> Summary of filter_spct [454 x 2] object: anonymous
#> Wavelength range 240-800 nm, step 1-4 nm
#> Label: Polyester, clear film, 0.000125 m thick, Autostat CT5 from McDermit Autotype; new
#> Variables:
#> w.length: Wavelength [nm]
#> Tfr: Total spectral transmittance [/1]
#> --
#> w.length Tfr
#> Min. :240.0 Min. :0.0030
#> 1st Qu.:376.2 1st Qu.:0.8920
#> Median :513.5 Median :0.9140
#> Mean :519.1 Mean :0.7835
#> 3rd Qu.:661.8 3rd Qu.:0.9211
#> Max. :800.0 Max. :0.9254
#>
#> $spct_2
#> Summary of filter_spct [425 x 2] object: anonymous
#> Wavelength range 190-800 nm, step 1-4 nm
#> Label: Theatrical 'gel', type 'Canary Supergel no312; new; from Rosco, UK
#> Variables:
#> w.length: Wavelength [nm]
#> Tfr: Total spectral transmittance [/1]
#> --
#> w.length Tfr
#> Min. :190.0 Min. :0.00001
#> 1st Qu.:314.0 1st Qu.:0.00001
#> Median :473.0 Median :0.01421
#> Mean :472.4 Mean :0.37195
#> 3rd Qu.:603.0 3rd Qu.:0.89521
#> Max. :800.0 Max. :0.90179
#>
summary(two_filters.spct, expand = "collection")
#> Summary of filter_mspct [2 x 1] object: anonymous
#> # A tibble: 2 × 8
#> spct.idx class dim w.length.min w.length.max colnames multiple.wl Tfr.type
#> <chr> <chr> <chr> <int> <int> <list> <dbl> <chr>
#> 1 spct_1 filter… [454… 240 800 <chr> 1 total
#> 2 spct_2 filter… [425… 190 800 <chr> 1 total
summary(two_filters.spct, expand = "auto") # <= 4 spectra
#> $spct_1
#> Summary of filter_spct [454 x 2] object: anonymous
#> Wavelength range 240-800 nm, step 1-4 nm
#> Label: Polyester, clear film, 0.000125 m thick, Autostat CT5 from McDermit Autotype; new
#> Variables:
#> w.length: Wavelength [nm]
#> Tfr: Total spectral transmittance [/1]
#> --
#> w.length Tfr
#> Min. :240.0 Min. :0.0030
#> 1st Qu.:376.2 1st Qu.:0.8920
#> Median :513.5 Median :0.9140
#> Mean :519.1 Mean :0.7835
#> 3rd Qu.:661.8 3rd Qu.:0.9211
#> Max. :800.0 Max. :0.9254
#>
#> $spct_2
#> Summary of filter_spct [425 x 2] object: anonymous
#> Wavelength range 190-800 nm, step 1-4 nm
#> Label: Theatrical 'gel', type 'Canary Supergel no312; new; from Rosco, UK
#> Variables:
#> w.length: Wavelength [nm]
#> Tfr: Total spectral transmittance [/1]
#> --
#> w.length Tfr
#> Min. :190.0 Min. :0.00001
#> 1st Qu.:314.0 1st Qu.:0.00001
#> Median :473.0 Median :0.01421
#> Mean :472.4 Mean :0.37195
#> 3rd Qu.:603.0 3rd Qu.:0.89521
#> Max. :800.0 Max. :0.90179
#>
summary(sun_evening.spct, expand = "auto") # > 4 spectra
#> Summary of source_mspct [5 x 1] object: anonymous
#> # A tibble: 5 × 8
#> spct.idx class dim w.length.min w.length.max colnames multiple.wl time.unit
#> <chr> <chr> <chr> <dbl> <dbl> <list> <dbl> <chr>
#> 1 time.01 sourc… [1,5… 290 1000. <chr> 1 second
#> 2 time.02 sourc… [1,5… 290 1000. <chr> 1 second
#> 3 time.03 sourc… [1,5… 290 1000. <chr> 1 second
#> 4 time.04 sourc… [1,5… 290 1000. <chr> 1 second
#> 5 time.05 sourc… [1,5… 290 1000. <chr> 1 second
where_measured(sun.spct)
#> # A tibble: 1 × 3
#> lat lon address
#> <dbl> <dbl> <chr>
#> 1 60.2 25.0 Kumpula, Helsinki, FI
where_measured(summary(sun.spct))
#> # A tibble: 1 × 3
#> lat lon address
#> <dbl> <dbl> <chr>
#> 1 60.2 25.0 Kumpula, Helsinki, FI
what_measured(summary(two_filters.spct))
#> $spct_1
#> [1] "Polyester, clear film, 0.000125 m thick, Autostat CT5 from McDermit Autotype; new"
#>
#> $spct_2
#> [1] "Theatrical 'gel', type 'Canary Supergel no312; new; from Rosco, UK"
#>
what_measured(summary(two_filters.spct, expand = "each")[[1]])
#> [1] "Polyester, clear film, 0.000125 m thick, Autostat CT5 from McDermit Autotype; new"
summary(sun_evening.mspct)
#> Summary of source_mspct [5 x 1] object: sun_evening.mspct
#> # A tibble: 5 × 8
#> spct.idx class dim w.length.min w.length.max colnames multiple.wl time.unit
#> <chr> <chr> <chr> <dbl> <dbl> <list> <dbl> <chr>
#> 1 time.01 sourc… [1,5… 290 1000. <chr> 1 second
#> 2 time.02 sourc… [1,5… 290 1000. <chr> 1 second
#> 3 time.03 sourc… [1,5… 290 1000. <chr> 1 second
#> 4 time.04 sourc… [1,5… 290 1000. <chr> 1 second
#> 5 time.05 sourc… [1,5… 290 1000. <chr> 1 second
summary(sun_evening.mspct, which.metadata = "when.measured")
#> Summary of source_mspct [5 x 1] object: sun_evening.mspct
#> # A tibble: 5 × 7
#> spct.idx class dim w.length.min w.length.max colnames when.measured
#> <chr> <chr> <chr> <dbl> <dbl> <list> <dttm>
#> 1 time.01 source_… [1,5… 290 1000. <chr> 2023-06-12 18:38:00
#> 2 time.02 source_… [1,5… 290 1000. <chr> 2023-06-12 18:39:00
#> 3 time.03 source_… [1,5… 290 1000. <chr> 2023-06-12 18:40:00
#> 4 time.04 source_… [1,5… 290 1000. <chr> 2023-06-12 18:41:00
#> 5 time.05 source_… [1,5… 290 1000. <chr> 2023-06-12 18:42:00
summary(two_filters.mspct, which.metadata = "what.measured")
#> Summary of filter_mspct [2 x 1] object: two_filters.mspct
#> # A tibble: 2 × 7
#> spct.idx class dim w.length.min w.length.max colnames what.measured
#> <chr> <chr> <chr> <int> <int> <list> <chr>
#> 1 spct_1 filter_spct [454 x … 240 800 <chr> Polyester, c…
#> 2 spct_2 filter_spct [425 x … 190 800 <chr> Theatrical '…
summary(two_filters.mspct, expand = "each")
#> $spct_1
#> Summary of filter_spct [454 x 2] object: anonymous
#> Wavelength range 240-800 nm, step 1-4 nm
#> Label: Polyester, clear film, 0.000125 m thick, Autostat CT5 from McDermit Autotype; new
#> Variables:
#> w.length: Wavelength [nm]
#> Tfr: Total spectral transmittance [/1]
#> --
#> w.length Tfr
#> Min. :240.0 Min. :0.0030
#> 1st Qu.:376.2 1st Qu.:0.8920
#> Median :513.5 Median :0.9140
#> Mean :519.1 Mean :0.7835
#> 3rd Qu.:661.8 3rd Qu.:0.9211
#> Max. :800.0 Max. :0.9254
#>
#> $spct_2
#> Summary of filter_spct [425 x 2] object: anonymous
#> Wavelength range 190-800 nm, step 1-4 nm
#> Label: Theatrical 'gel', type 'Canary Supergel no312; new; from Rosco, UK
#> Variables:
#> w.length: Wavelength [nm]
#> Tfr: Total spectral transmittance [/1]
#> --
#> w.length Tfr
#> Min. :190.0 Min. :0.00001
#> 1st Qu.:314.0 1st Qu.:0.00001
#> Median :473.0 Median :0.01421
#> Mean :472.4 Mean :0.37195
#> 3rd Qu.:603.0 3rd Qu.:0.89521
#> Max. :800.0 Max. :0.90179
#>