A quick start to the spectacles package

Pierre Roudier

2025-10-20

library(spectacles)

Converting data to a SpectraDataFrame

data("australia")
class(australia)
#> [1] "data.frame"
big.head(australia)
#>   sr_no carbon  ph clay       X350 ...     X2496     X2497     X2498     X2499
#> 1    28   0.63 7.3 30.0 0.08173233 ... 0.3888433 0.3942973 0.3934600 0.3889097
#> 2    36   0.69 9.4 45.0 0.10344727 ... 0.3035470 0.3016855 0.3077460 0.3116423
#> 3   136   1.44 8.9 33.3 0.11363971 ... 0.3524803 0.3526042 0.3598545 0.3576893
#> 4   194   0.33 7.2  3.5 0.16374375 ... 0.7547905 0.7552416 0.7525422 0.7513548
#> 5   215   1.12 8.1 17.1 0.09693917 ... 0.4397273 0.4433315 0.4389216 0.4340123
#>       X2500
#> 1 0.3864646
#> 2 0.3036998
#> 3 0.3460697
#> 4 0.7567009
#> 5 0.4373087
spectra(australia) <- sr_no ~ ... ~ 350:2500
#> Wavelength range: 350 to 2500 nm
#> Spectral resolution: 1 nm
summary(australia)
#> Object of class SpectraDataFrame
#> Set of 100 spectra
#> Wavelength range: 350 to 2500 nm
#> Spectral resolution: 1 nm
#> Data attributes:
#>      carbon            ph             clay      
#>  Min.   :0.050   Min.   :5.000   Min.   : 2.80  
#>  1st Qu.:0.780   1st Qu.:6.200   1st Qu.:18.15  
#>  Median :1.365   Median :7.300   Median :33.65  
#>  Mean   :2.305   Mean   :7.196   Mean   :35.80  
#>  3rd Qu.:3.135   3rd Qu.:8.025   3rd Qu.:50.98  
#>  Max.   :9.530   Max.   :9.500   Max.   :69.00

Accessing the different elements of the SpectraDataFrame object

General information about the SpectraDataFrame

nrow returns the number of samples in the object:

nrow(australia)
#> [1] 100

ncol returns the number of attributes in the data slot of the object, and returns NULL if the object does not have associated data:

ncol(australia)
#> [1] 2151

length returns the number of wavelengths in the object:

length(australia)
#> [1] 2151

dim returns a numeric vector of these three dimensions:

dim(australia)
#> [1]  100 2151    3

Subsetting

sub <- australia[1:5,]
summary(sub)
#> Object of class SpectraDataFrame
#> Set of 5 spectra
#> Wavelength range: 350 to 2500 nm
#> Spectral resolution: 1 nm
#> Data attributes:
#>      carbon            ph            clay      
#>  Min.   :0.330   Min.   :7.20   Min.   : 3.50  
#>  1st Qu.:0.630   1st Qu.:7.30   1st Qu.:17.10  
#>  Median :0.690   Median :8.10   Median :30.00  
#>  Mean   :0.842   Mean   :8.18   Mean   :25.78  
#>  3rd Qu.:1.120   3rd Qu.:8.90   3rd Qu.:33.30  
#>  Max.   :1.440   Max.   :9.40   Max.   :45.00

Accessing specific properties of Spectra objects

Specific functions are available to access the various properties of Spectra objects:

ids is returning a vector containing the IDs of the object. It has a as.vector option. When turned to FALSE, the function returns a data.frame instead of a vector. This is particularly useful to retrieve the original column name of the IDs:

# Just printing the first 5
ids(australia)[1:5]
#> [1]  28  36 136 194 215

wl is returning the wavelengths of the object in a numeric vector:

# Just printing the first 10
wl(australia)[1:10]
#>  [1] 350 351 352 353 354 355 356 357 358 359

spectra is returning the spectra matrix:

s <- spectra(australia)
class(s)
#> [1] "matrix" "array"
dim(s)
#> [1]  100 2151
big.head(s)
#>           X350       X351       X352       X353       X354 ...     X2496
#> 28  0.08173233 0.08074037 0.08312159 0.08690414 0.08761925 ... 0.3888433
#> 36  0.10344727 0.09767456 0.09267905 0.09155867 0.10600654 ... 0.3035470
#> 136 0.11363971 0.13762568 0.14234437 0.13608806 0.13451828 ... 0.3524803
#> 194 0.16374375 0.16650400 0.16646151 0.16540240 0.16768558 ... 0.7547905
#> 215 0.09693917 0.10563760 0.10342025 0.09727478 0.10408881 ... 0.4397273
#>         X2497     X2498     X2499     X2500
#> 28  0.3942973 0.3934600 0.3889097 0.3864646
#> 36  0.3016855 0.3077460 0.3116423 0.3036998
#> 136 0.3526042 0.3598545 0.3576893 0.3460697
#> 194 0.7552416 0.7525422 0.7513548 0.7567009
#> 215 0.4433315 0.4389216 0.4340123 0.4373087

wl_units is returning the wavelength units:

wl_units(australia)
#> [1] "nm"

features is returning associated data into a data.frame:

df <- features(australia)
class(df)
#> [1] "data.frame"
head(df)
#>     carbon  ph clay
#> 28    0.63 7.3 30.0
#> 36    0.69 9.4 45.0
#> 136   1.44 8.9 33.3
#> 194   0.33 7.2  3.5
#> 215   1.12 8.1 17.1
#> 244   1.14 8.1 34.0

Basic plotting

plot(australia)

plot(australia, col = "royalblue")