photobiology (version 0.11.1)

smooth_spct: Smooth a spectrum

Description

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, ...)

# S3 method for default smooth_spct(x, method, strength, wl.range, ...)

# S3 method for source_spct smooth_spct( x, method = "custom", strength = 1, wl.range = NULL, na.rm = FALSE, ... )

# S3 method for filter_spct smooth_spct( x, method = "custom", strength = 1, wl.range = NULL, na.rm = FALSE, ... )

# S3 method for reflector_spct smooth_spct( x, method = "custom", strength = 1, wl.range = NULL, na.rm = FALSE, ... )

# S3 method for solute_spct smooth_spct( x, method = "custom", strength = 1, wl.range = NULL, na.rm = FALSE, ... )

# S3 method for response_spct smooth_spct( x, method = "custom", strength = 1, wl.range = NULL, na.rm = FALSE, ... )

# S3 method for cps_spct smooth_spct( x, method = "custom", strength = 1, wl.range = NULL, na.rm = FALSE, ... )

# S3 method for generic_mspct smooth_spct( x, method = "custom", strength = 1, wl.range = NULL, na.rm = FALSE, ... )

Value

A copy of x with spectral data values replaced by smoothed ones.

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. NA is interpreted as the min or max value of x[[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 function

  • smooth_spct(source_spct): Smooth a source spectrum

  • smooth_spct(filter_spct): Smooth a filter spectrum

  • smooth_spct(reflector_spct): Smooth a reflector spectrum

  • smooth_spct(solute_spct): Smooth a solute attenuation spectrum

  • smooth_spct(response_spct): Smooth a response spectrum

  • smooth_spct(cps_spct): Smooth a counts per second spectrum

  • smooth_spct(generic_mspct):

Examples

Run this code

my.spct <- clip_wl(sun.spct, c(400, 500))
smooth_spct(my.spct)
smooth_spct(my.spct, method = "custom", strength = 1)
smooth_spct(my.spct, method = "custom", strength = 4)
smooth_spct(my.spct, method = "supsmu", strength = 4)

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