spec-class: Class "spec" for the storage of spectral models.

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

Class "spec" for the storage of spectral models.

Description

spec is the class for spectral models; an object of class "mass" is initialized if mod_type = "spec" is an argument of initModel. All objects of class spec are also of class dat; see documentation for dat for a description of these slots. Note that here x2 will refer to the independent variable in which traces are resolved, e.g., wavelength or wavenumber.

Objects from the Class

Objects can be created by calls of the form new("spec", ...) or spec(...).

Slots

clpequ:

Object of class "vector" of starting values for linear relationships between clp

specpar:

Object of class "list" of vectors of starting values for spectral parameters; the number of vectors gives the number of components in the resulting spectral model; each vector contains the parameters associated with a component. e.g., specpar = list(c(20000, 3000, .3, 21000, 2000, .4), c(18000, 1000, .2)); the parameters in each vector are grouped c(location_spectra, width_spectra, skew_spectra). the location and width parameters are given in wavenumbers.

specfun:

Object of class "character", "gaus" for a spectral model of a superposition of skewed Gaussians; "bspline" for a bspline-based model.

specref:

Object of class "numeric" index defining the center value of the x2 variable.

specCon:

Object of class "list" used internally to store constraints.

specdisp:

Object of class "logical" TRUE if time-dependence of the spectral parameters is to be taken into account and FALSE otherwise

specdisppar:

Object of class "list"

specdispindex:

Object of class "list" of vectors defining those indexes of specpar whose time-dependence is to be modeled. e.g., specdispindex = list(c(1,1), c(1,2), c(1,3)) says that parameters 1-3 of spectra 1 are to be modeled as time-dependent.

nupow:

Object of class "numeric" describing the power to which wavenumbers are raised in the model equation; see Equation 30 of the paper in the references section for a complete description

timedep:

Object of class "logical" describing whether the model for spectra E is dependent on x-index (i.e., whether it is clp-dependent).

parmufunc:

Object of class "character" describing the function form of the time-dependence of spectral parameters; options are "exp" for exponential time dependence, "multiexp" for multiexponential time dependence, and "poly" for polynomial time dependence. defaults to polynomial time dependence.

ncole

vector describing the number of columns of the E matrix for each value in the x vector

Extends

Class dat-class, directly.

Author(s)

Katharine M. Mullen, Ivo H. M. van Stokkum

References

Ivo H. M. van Stokkum, "Global and target analysis of time-resolved spectra, Lecture notes for the Troisieme Cycle de la Physique en Suisse Romande", Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands, 2005, https://www.nat.vu.nl/~ivo/pub/2005/lecturenotes3cycle.pdf

See Also

kin-class, dat-class

TIMP documentation built on Dec. 28, 2022, 3:06 a.m.