Row-bind spectra — rbindspct • photobiology

A wrapper on dplyr::rbind_fill that preserves class and other attributes of spectral objects.

Usage

rbindspct(
  l,
  use.names = TRUE,
  fill = TRUE,
  idfactor = TRUE,
  attrs.source = NULL,
  attrs.simplify = FALSE
)

Arguments

l: A source_mspct, filter_mspct, reflector_mspct, response_mspct, chroma_mspct, cps_mspct, generic_mspct object or a list containing source_spct, filter_spct, reflector_spct, response_spct, chroma_spct, cps_spct, or generic_spct objects.
use.names: logical If TRUE items will be bound by matching column names. By default TRUE for rbindspct. Columns with duplicate names are bound in the order of occurrence, similar to base. When TRUE, at least one item of the input list has to have non-null column names.
fill: logical If TRUE fills missing columns with NAs. By default TRUE. When TRUE, use.names has also to be TRUE, and all items of the input list have to have non-null column names.
idfactor: logical or character Generates an index column of factor type. Default is (idfactor=TRUE) for both lists and _mspct objects. If idfactor=TRUE then the column is auto named spct.idx. Alternatively the column name can be directly provided to idfactor as a character string.
attrs.source: integer Index into the members of the list from which attributes should be copied. If NULL, all attributes are collected into named lists, except that unique comments are pasted.
attrs.simplify: logical Flag indicating that when all values of an attribute are equal for all members, the named list will be replaced by a single copy of the value.

Value

An spectral object of a type common to all bound items containing a concatenation of all the items passed in. If the argument 'idfactor' is TRUE, then a factor 'spct.idx' will be added to the returned spectral object.

Details

Each item of l should be a spectrum, including NULL (skipped) or an empty object (0 rows). rbindspc is most useful when there are a variable number of (potentially many) objects to stack. rbindspct always returns at least a generic_spct as long as all elements in l are spectra.

Note

Note that any additional 'user added' attributes that might exist on individual items of the input list will not be preserved in the result. The attributes used by the photobiology package are preserved, and if they are not consistent across the bound spectral objects, a warning is issued.

dplyr::rbind_fill is called internally and the result returned is the highest class in the inheritance hierarchy which is common to all elements in the list. If not all members of the list belong to one of the _spct classes, an error is triggered. The function sets all data in source_spct and response_spct objects supplied as arguments into energy-based quantities, and all data in filter_spct objects into transmittance before the row binding is done. If any member spectrum is tagged, it is untagged before row binding.

Examples

# default, adds factor 'spct.idx' with letters as levels
spct <- rbindspct(list(sun.spct, sun.spct))
spct
#> Object: source_spct [1,044 x 4]
#> containing 2 spectra in long form
#> Wavelength range 280-800 nm, step 0.9230769-1 nm 
#> spct_1 label: sunlight, simulated
#> spct_2 label: sunlight, simulated 
#> spct_1 measured on 2010-06-22 09:51:00 UTC
#> spct_2 measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI
#> 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] 
#> --
#> # A tibble: 1,044 × 4
#>    w.length s.e.irrad s.q.irrad spct.idx
#>       <dbl>     <dbl>     <dbl> <fct>   
#>  1     280          0         0 spct_1  
#>  2     281.         0         0 spct_1  
#>  3     282.         0         0 spct_1  
#>  4     283.         0         0 spct_1  
#>  5     284.         0         0 spct_1  
#>  6     285.         0         0 spct_1  
#>  7     286.         0         0 spct_1  
#>  8     286.         0         0 spct_1  
#>  9     287.         0         0 spct_1  
#> 10     288.         0         0 spct_1  
#> # ℹ 1,034 more rows
class(spct)
#> [1] "source_spct"  "generic_spct" "tbl_df"       "tbl"          "data.frame"  

# adds factor 'spct.idx' with letters as levels
spct <- rbindspct(list(sun.spct, sun.spct), idfactor = TRUE)
head(spct)
#> Object: source_spct [6 x 4]
#> Wavelength range 280-284.61538 nm, step 0.9230769 nm 
#> spct_1 label: sunlight, simulated 
#> spct_1 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] 
#> --
#> # A tibble: 6 × 4
#>   w.length s.e.irrad s.q.irrad spct.idx
#>      <dbl>     <dbl>     <dbl> <fct>   
#> 1     280          0         0 spct_1  
#> 2     281.         0         0 spct_1  
#> 3     282.         0         0 spct_1  
#> 4     283.         0         0 spct_1  
#> 5     284.         0         0 spct_1  
#> 6     285.         0         0 spct_1  
class(spct)
#> [1] "source_spct"  "generic_spct" "tbl_df"       "tbl"          "data.frame"  

# adds factor 'spct.idx' with the names given to the spectra in the list
# supplied as formal argument 'l' as levels
spct <- rbindspct(list(one = sun.spct, two = sun.spct), idfactor = TRUE)
head(spct)
#> Object: source_spct [6 x 4]
#> Wavelength range 280-284.61538 nm, step 0.9230769 nm 
#> one label: sunlight, simulated 
#> one 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] 
#> --
#> # A tibble: 6 × 4
#>   w.length s.e.irrad s.q.irrad spct.idx
#>      <dbl>     <dbl>     <dbl> <fct>   
#> 1     280          0         0 one     
#> 2     281.         0         0 one     
#> 3     282.         0         0 one     
#> 4     283.         0         0 one     
#> 5     284.         0         0 one     
#> 6     285.         0         0 one     
class(spct)
#> [1] "source_spct"  "generic_spct" "tbl_df"       "tbl"          "data.frame"  

# adds factor 'ID' with the names given to the spectra in the list
# supplied as formal argument 'l' as levels
spct <- rbindspct(list(one = sun.spct, two = sun.spct),
                  idfactor = "ID")
head(spct)
#> Object: source_spct [6 x 4]
#> Wavelength range 280-284.61538 nm, step 0.9230769 nm 
#> one label: sunlight, simulated 
#> one measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI
#> 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] 
#> --
#> # A tibble: 6 × 4
#>   w.length s.e.irrad s.q.irrad ID   
#>      <dbl>     <dbl>     <dbl> <fct>
#> 1     280          0         0 one  
#> 2     281.         0         0 one  
#> 3     282.         0         0 one  
#> 4     283.         0         0 one  
#> 5     284.         0         0 one  
#> 6     285.         0         0 one  
class(spct)
#> [1] "source_spct"  "generic_spct" "tbl_df"       "tbl"          "data.frame"