These functions implement one original methods and acts as a wrapper for other common R smoothing functions. The advantage of using this function for smoothing spectral objects is that it simplifies the user interface and sets, when needed, defaults suitable for spectral data.
Usage
smooth_spct(x, method, strength, wl.range, ...)
# Default S3 method
smooth_spct(x, method, strength, wl.range, ...)
# S3 method for class 'source_spct'
smooth_spct(
x,
method = "custom",
strength = 1,
wl.range = NULL,
na.rm = FALSE,
...
)
# S3 method for class 'filter_spct'
smooth_spct(
x,
method = "custom",
strength = 1,
wl.range = NULL,
na.rm = FALSE,
...
)
# S3 method for class 'reflector_spct'
smooth_spct(
x,
method = "custom",
strength = 1,
wl.range = NULL,
na.rm = FALSE,
...
)
# S3 method for class 'solute_spct'
smooth_spct(
x,
method = "custom",
strength = 1,
wl.range = NULL,
na.rm = FALSE,
...
)
# S3 method for class 'response_spct'
smooth_spct(
x,
method = "custom",
strength = 1,
wl.range = NULL,
na.rm = FALSE,
...
)
# S3 method for class 'cps_spct'
smooth_spct(
x,
method = "custom",
strength = 1,
wl.range = NULL,
na.rm = FALSE,
...
)
# S3 method for class 'generic_mspct'
smooth_spct(
x,
method = "custom",
strength = 1,
wl.range = NULL,
na.rm = FALSE,
...
)Arguments
- x
an R object.
- method
a character string "custom", "lowess", "supsmu" or "skip"..
- strength
numeric value to adjust the degree of smoothing. Ignored if method-specific parameters are passed through
....- wl.range
any R object on which applying the method
range()yields a vector of two numeric values, describing a range of wavelengths (nm) within which spectral data is to be smoothed.NAis interpreted as the min or max value ofx[[w.length]].- ...
other parameters passed to the underlying smoothing functions.
- na.rm
logical A flag indicating whether NA values should be stripped before the computation proceeds.
Methods (by class)
smooth_spct(default): Default for generic functionsmooth_spct(source_spct): Smooth a source spectrumsmooth_spct(filter_spct): Smooth a filter spectrumsmooth_spct(reflector_spct): Smooth a reflector spectrumsmooth_spct(solute_spct): Smooth a solute attenuation spectrumsmooth_spct(response_spct): Smooth a response spectrumsmooth_spct(cps_spct): Smooth a counts per second spectrumsmooth_spct(generic_mspct):
Note
Method "custom" is our home-brewed method which applies strong
smoothing to low signal regions of the spectral data, and weaker or no
smoothing to the high signal areas. Values very close to zero are set to
zero with a limit which depends on the local variation. This method is an
ad-hock method suitable for smoothing spectral data obtained with
spectrometers. In the cased of methods "lowess" and "supsmu" the current
function behaves like a wrapper of the functions of the same names from
base R. Method "skip" returns x unchanged.
Examples
my.spct <- clip_wl(sun.spct, c(400, 500))
smooth_spct(my.spct)
#> Object: source_spct [101 x 3]
#> Wavelength range 400-500 nm, step 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]
#> --
#> # A tibble: 101 × 3
#> w.length s.e.irrad s.q.irrad
#> <dbl> <dbl> <dbl>
#> 1 400 0.608 0.00000203
#> 2 401 0.626 0.00000210
#> 3 402 0.650 0.00000218
#> 4 403 0.621 0.00000209
#> 5 404 0.637 0.00000215
#> 6 405 0.626 0.00000212
#> 7 406 0.600 0.00000204
#> 8 407 0.595 0.00000202
#> 9 408 0.626 0.00000213
#> 10 409 0.662 0.00000226
#> # ℹ 91 more rows
smooth_spct(my.spct, method = "custom", strength = 1)
#> Object: source_spct [101 x 3]
#> Wavelength range 400-500 nm, step 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]
#> --
#> # A tibble: 101 × 3
#> w.length s.e.irrad s.q.irrad
#> <dbl> <dbl> <dbl>
#> 1 400 0.608 0.00000203
#> 2 401 0.626 0.00000210
#> 3 402 0.650 0.00000218
#> 4 403 0.621 0.00000209
#> 5 404 0.637 0.00000215
#> 6 405 0.626 0.00000212
#> 7 406 0.600 0.00000204
#> 8 407 0.595 0.00000202
#> 9 408 0.626 0.00000213
#> 10 409 0.662 0.00000226
#> # ℹ 91 more rows
smooth_spct(my.spct, method = "custom", strength = 4)
#> Object: source_spct [101 x 3]
#> Wavelength range 400-500 nm, step 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]
#> --
#> # A tibble: 101 × 3
#> w.length s.e.irrad s.q.irrad
#> <dbl> <dbl> <dbl>
#> 1 400 0.608 0.00000203
#> 2 401 0.626 0.00000210
#> 3 402 0.650 0.00000218
#> 4 403 0.621 0.00000209
#> 5 404 0.637 0.00000215
#> 6 405 0.626 0.00000212
#> 7 406 0.600 0.00000204
#> 8 407 0.595 0.00000202
#> 9 408 0.626 0.00000213
#> 10 409 0.662 0.00000226
#> # ℹ 91 more rows
smooth_spct(my.spct, method = "supsmu", strength = 4)
#> Object: source_spct [101 x 3]
#> Wavelength range 400-500 nm, step 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]
#> --
#> # A tibble: 101 × 3
#> w.length s.e.irrad s.q.irrad
#> <dbl> <dbl> <dbl>
#> 1 400 0.629 0.00000210
#> 2 401 0.627 0.00000210
#> 3 402 0.625 0.00000210
#> 4 403 0.623 0.00000210
#> 5 404 0.621 0.00000210
#> 6 405 0.627 0.00000212
#> 7 406 0.620 0.00000210
#> 8 407 0.620 0.00000211
#> 9 408 0.626 0.00000213
#> 10 409 0.627 0.00000214
#> # ℹ 91 more rows