R: Mean from collection of spectra

s_mean {photobiology}

R Documentation

Mean from collection of spectra

Description

A method to compute the mean of values across members of a collections of spectra. Computes the mean at each wavelength across all the spectra in the collection returning a spectral object.

Usage

s_mean(x, trim, na.rm, ...)

## Default S3 method:
s_mean(x, trim = 0, na.rm = FALSE, ...)

## S3 method for class 'source_mspct'
s_mean(x, trim = 0, na.rm = FALSE, ...)

## S3 method for class 'response_mspct'
s_mean(x, trim = 0, na.rm = FALSE, ...)

## S3 method for class 'filter_mspct'
s_mean(x, trim = 0, na.rm = FALSE, ...)

## S3 method for class 'reflector_mspct'
s_mean(x, trim = 0, na.rm = FALSE, ...)

## S3 method for class 'calibration_mspct'
s_mean(x, trim = 0, na.rm = FALSE, ...)

## S3 method for class 'cps_mspct'
s_mean(x, trim = 0, na.rm = FALSE, ...)

## S3 method for class 'raw_mspct'
s_mean(x, trim = 0, na.rm = FALSE, ...)

Arguments

`x`	An R object Currently this package defines methods for collections of spectral objects.
`trim`	numeric The fraction (0 to 0.5) of observations to be trimmed from each end of x before the mean is computed. Values of trim outside that range are taken as the nearest endpoint.
`na.rm`	logical A value indicating whether NA values should be stripped before the computation proceeds.
`...`	Further arguments passed to or from other methods.

Value

If x is a collection spectral of objects, such as a "filter_mspct" object, the returned object is of same class as the members of the collection, such as "filter_spct", containing the mean spectrum.

Methods (by class)

s_mean(default):
s_mean(source_mspct):
s_mean(response_mspct):
s_mean(filter_mspct):
s_mean(reflector_mspct):
s_mean(calibration_mspct):
s_mean(cps_mspct):
s_mean(raw_mspct):

Note

Trimming of extreme values and omission of NAs is done separately at each wavelength. Interpolation is not applied, so all spectra in x must share the same set of wavelengths.

Objects of classes raw_spct and cps_spct can contain data from multiple scans. This functions are implemented for these classes only for the case when all member spectra contain data for a single scan, or spliced into a single column in the case of cps_spct members.