residPart-methods

residPart

residPart,kin-method

residPart,spec-method

residPart,mass-method

residPart,amp-method

Methods for function <code>residPart</code> in Package `TIMP' determine the 
part of the residual vector associated with a single `part' of the
dataset(s).

methods

A problem solving environment (PSE) for fitting separable
nonlinear models to measurements arising in physics and chemistry
experiments, as described by Mullen & van Stokkum (2007)
<doi:10.18637/jss.v018.i03> for its use in fitting time resolved
spectroscopy data, and as described by Laptenok et al. (2007)
<doi:10.18637/jss.v018.i08> for its use in fitting Fluorescence
Lifetime Imaging Microscopy (FLIM) data, in the study of Förster
Resonance Energy Transfer (FRET). `TIMP` also serves as the
computation backend for the `GloTarAn` software, a graphical user
interface for the package, as described in Snellenburg et al. (2012)
<doi:10.18637/jss.v049.i03>.

Joris J Snellenburg

TIMP

Fitting Separable Nonlinear Models in Spectroscopy and
Microscopy

Katharine M. Mullen

Joris Snellenburg

Sergey P. Laptenok

David Nicolaides

Ivo H.M. van Stokkum

residPart-methods function

<dl> <dt>model</dt>
<dd>Object of class <code>dat</code>; switches on this 
argument.</dd> <dt>group</dt>
<dd>list of vector pairs (x2 index, dataset index) for which 
the part of the residual vector is to be determined</dd> <dt>multimodel</dt>
<dd>Object of class <code>multimodel</code></dd>
 
 <dt>thetalist</dt>
<dd>Object of class <code>multitheta</code></dd>
 
 <dt>clpindepX</dt>
<dd>Object of class <code>matrix</code> containing the matrix
 determined directly by the nonlinear parameters (e.g., a concentration matrix
in the case of a kinetic model) in the case that this matrix does not depend
on the <code>x2</code> index</dd>
 
 <dt>finished</dt>
<dd>logical determining whether fitting is finished that
 triggers the storage of results</dd>
 
 <dt>returnX</dt>
<dd>logical determining whether to just return the matrix 
<code>X</code> directly dependent on nonlinear parameters; this is used in the finite
difference derivative of <code>X</code> used to get standard error estimates on the 
conditionally linear parameters.</dd><dt>rawtheta</dt>
<dd>numeric vector of nonlinear parameters to be optimized 
by <code>nls</code>; this is used in the finite
difference derivative of <code>X</code> used to get standard error estimates on the 
conditionally linear parameters.</dd>
 
</dl>

Arguments

Generic function residPart in Package `TIMP' — residPart-methods

<dl>

 <dt>model</dt>
<dd>Object of class <code>dat</code>; switches on this 
argument.</dd>

 <dt>group</dt>
<dd>list of vector pairs (x2 index, dataset index) for which 
the part of the residual vector is to be determined</dd>

 <dt>multimodel</dt>
<dd>Object of class <code>multimodel</code></dd>
 
 <dt>thetalist</dt>
<dd>Object of class <code>multitheta</code></dd>
 
 <dt>clpindepX</dt>
<dd>Object of class <code>matrix</code> containing the matrix
 determined directly by the nonlinear parameters (e.g., a concentration matrix
in the case of a kinetic model) in the case that this matrix does not depend
on the <code>x2</code> index</dd>
 
 <dt>finished</dt>
<dd>logical determining whether fitting is finished that
 triggers the storage of results</dd>
 
 <dt>returnX</dt>
<dd>logical determining whether to just return the matrix 
<code>X</code> directly dependent on nonlinear parameters; this is used in the finite
difference derivative of <code>X</code> used to get standard error estimates on the 
conditionally linear parameters.</dd>

<dt>rawtheta</dt>
<dd>numeric vector of nonlinear parameters to be optimized 
by <code>nls</code>; this is used in the finite
difference derivative of <code>X</code> used to get standard error estimates on the 
conditionally linear parameters.</dd>
 
</dl>

Generic function residPart in Package `TIMP'

residPart-methods: Generic function residPart in Package `TIMP'

Description

Usage

Arguments

See Also