kinopt-class: Class "kinopt" stores options for fitting and plotting...

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

Class "kinopt" stores options for fitting and plotting kinetic models

Description

Class "kinopt" stores options for fitting and plotting kinetic models in particular; this is a subclass of class opt

Details

See opt-class for the specification of fitting/plotting options that are not specific to the class type.

Objects from the Class

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

Slots

notraces:

Object of class "logical" that defaults to FALSE; if TRUE, do not plot traces

selectedtraces:

Object of class "vector" containing x indices for which plots of traces are desired under a kinetic model

breakdown:

Object of class "list" with the following elements:

• plotvector of x2 values to plot the breakdown for. These values be specified in a fuzzy way: an x2 value within abs(x2[1] - x2[2])/100 a value given in plot means that a plot for that x2 value will be generated, where the reference x2[1] and x2[2] are from the first dataset modeled.

• tolnumeric giving a tolerance by which the values in plot are compared to x2 values for near-equality. The default is defined as abs(x2[1] - x2[2])/100.

• superimposevector of dataset indices for which results should be superimposed if the dataset has an x2 value at a value in plot.

FLIM

Object of class "logical" that defaults to FALSE; if TRUE, the data represent a FLIM experiment and special plots are generated.

FLIMresidimag

Object of class "logical" that defaults to TRUE; if FALSE and a FLIM image is analyzed, the residuals are not plotted as an image.

noFLIMsummary

Object of class "logical" that defaults to FALSE; if TRUE and a FLIM image is analyzed, only other plots requested by the user (such as traces or residuals) are generated, and no summary plot in made.

kinspecest

Object of class "logical" that defaults to FALSE; if TRUE, make a plot of the spectra associated with the kinetic components as well as the lifetime estimates.

writeplaincon

Object of class "list"; if length is greater than 0, then the concentration model will be evaluated at the vector of x values supplied as the element "x" of writeplaincon and the result will be written to file for each dataset.

writerawcon

Object of class "logical" that defaults to FALSE; if TRUE, then the representation of the concentration profiles before the application of constraints (to account for the equality of spectra, etc.) is written to file for each dataset.

plotcohcolspec

Object of class "logical" that defaults to TRUE; if FALSE then the spectra associated with the coherent artifact (pulse-follower) are not included in the summary plots

plotpulsefol:

Object of class "logical" defaults to FALSE; if TRUE adding imageplots of pulsefolower amplitudes in summary plot (only with FLIM plots).

ylimcomp

Object of class "vector" that defaults to vector(); Works In the case of plotting the results of FLIM image analysis, ylimspec can be used to determine the range used in the image plot of normalized amplitudes.

addfilename

addest

adddataimage

algorithm

coldata

colfit

divdrel

getStartTri

imagepal

iter

kinspecerr

linrange

ltydata

ltyfit

makeps

maxfev

minFactor

nlsalgorithm

nnls

nnlscrit

noplotest

normspec

optimmethod

output

paropt

parscale

plot

plotkinspec

residplot

residtraces

samespecline

specinterpol

specinterpolbspline

specinterpolpoints

specinterpolseg

stderrclp

summaryplotcol

summaryplotrow

sumnls

superimpose

title

trilinear

triStart

writeclperr

writecon

writedata

writefit

writefitivo

writenormspec

writespec

writespecinterpol

xlab

xlim

xlimspec

ylab

ylimspec

ylimspecplus

Author(s)

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

See Also

examineFit, fitModel, opt-class, specopt-class

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