set_absolute_bounds: Set absolute bounds on an NMRScaffold1D or NMRScaffold2D...

In ssokolen/rnmrfit: Robust NMR Lineshape Fitting in the Frequency Domain

Description

Although any NMRScaffold object can act as a boundary on another NMRScaffold object, this function provides a convenience method for generating such bounds using a simple set of lower and upper constraints on basic peak parameters such as position, height, width, etc... Note that the term "absolute" refers to the fact that the same bounds are applied to each and every peak, regardless of current parameter values. However, these bounds can still be normalized to the data using the normalized argument.

Usage

set_absolute_bounds(object, position = NULL, height = NULL,
  width = NULL, baseline = NULL, phase = NULL, normalized = FALSE,
  peak.units = "hz", widen = FALSE, ...)

## S4 method for signature 'NMRScaffold1D'
set_absolute_bounds(object, position = NULL,
  height = NULL, width = NULL, baseline = NULL, phase = NULL,
  normalized = FALSE, peak.units = "hz", widen = FALSE)

Arguments

object	An NMRScaffold1D or NMRscaffold2D object. NMR data must be attached to object to enable normalization.
position	A vector of two elements corresponding to a lower and upper bound for peak position. If the normalized argument is true, 0 corresponds to the leftmost range of the data and 1 to the rightmost. Otherwise, the units are in ppm.
height	A vector of two elements corresponding to a lower and upper bound for peak height. If the normalized argument is true, 0 corresponds to the lowest value of spectral intensity and 1 to the largest. Otherwise, the units correspond to arbitrary spectral intensity values.
width	A vector of two elements corresponding to a lower and upper bound for peak width. If the normalized argument is true, 0 corresponds to the leftmost range of the data and 1 to the rightmost. Otherwise, the units depend on the peak.units argument.
baseline	A vector of two elements corresponding to a lower and upper bound for baseline height. If the normalized argument is true, 0 corresponds to the lowest value of spectral intensity and 1 to the largest. Otherwise, the units correspond to arbitrary spectral intensity values. The same constraints are applied to the real baseline and the imaginary baseline difference.
phase	A vector of two elements corresponding to a lower and upper bound for phase in radians.
normalized	TRUE to set bounds in terms of the underlying data, where the x and y values of the data are scaled between 0 and 1. FALSE to use natural units of ppm/Hz and spectral intensity.
peak.units	The units of peak width – either 'ppm' or 'hz'.
widen	FALSE to prevent new bounds from widening existing bounds.
...	Additional arguments passed to inheriting methods.

Details

In practice, absolute bounds are primarily useful for preventing very large phase deviations, preventing the baseline from attempting to fit peaks and putting a hard constraint on peak widths.

Value

A new NMRScaffold1D or NMRScaffold2D object with modified parameters.

ssokolen/rnmrfit documentation built on May 23, 2019, 1:48 p.m.