nmrscaffold_1d: Generate an NMRScaffold1D object based on simplified peak...

Description Usage Arguments Details Value

View source: R/NMRScaffold1D.R

Description

Generates an NMRScaffold1D object by converting multiplet definitions into a set of singlets related by constraints on their position and area. height and convert coupling constants from Hz to ppm. If no data is provided, peak heights are assumed to be 0. This is a bad initial guess and is unlikely to result in a good fit.

Usage

1
2
3
nmrscaffold_1d(peak.list, nmrdata, peak.type = "lorenz",
  peak.width = 1, baseline.degree = 3, n.knots = 3,
  include.difference = TRUE, include.phase = TRUE, store = TRUE)

Arguments

peak.list

A vector or list of character strings specifying multiplets of the form "3 d 1.2". See details section.

nmrdata

An NMRData1D object.

peak.type

One of lorenz, gauss, pvoigt, or voigt.

peak.width

Initial estimate of peak width (in Hz)

baseline.degree

Degree of B-spline polynomials to use for baseline. As the degree can be 0, use NULL to remove baseline entirely (default value).

n.knots

The number of equally spaced interior knots used for B-spline baseline. The knots can be changed after the scaffold in initialized.

include.difference

Include a baseline difference term to account for slight difference between real and imaginary components. By default, this difference is initialized to be the same as the baseline term. This can be changed later.

include.phase

Include a phasing term in the fit.

store

FALSE to not store the nmrdata object. Although storing an nmrdata object is likely to be more convenient, it may result in unnecessary data copies.

Details

Multiplets are specified in the from of "3 d 1.2", which indicates a doublet at 3 ppm, with a coupling constant of 1.2 Hz. Supported multiplet codes include s, d, t, q, quint, sext, sept, oct, dd, dt, td, and tt. The latter 4 expect two coupling values. The exact syntax of the specification is quite flexible, as the function removes all brackets and most punctuation and converts common spacers like - and _ into whitespace. Satellite coupling constants (in Hz) can be added using "j" in the specification, so "3 s j 10" would indicate a singlet at 3 ppm and 1 pair of satellites with a coupling constant of 10 Hz. It's also possible to offset the center of the satellite doublet from the center of the main isotopic peak using a colon. In the specification of "3 s j 10:0.01", the center of the satellite doublet is offset 0.01 ppm upfield.

Value

An NMRScaffold1D object.


ssokolen/rnmrfit documentation built on Nov. 23, 2018, 12:25 a.m.