Class "kinopt" stores options for fitting and plotting kinetic models
Class "kinopt" stores options for fitting and plotting kinetic models in particular; this is a subclass of class opt
class
Objects can be created by calls of the form new("kinopt", ...) or kinopt(...)
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:
See opt-class for the specification of fitting/plotting options that are not specific to the class type.
Katharine M. Mullen, Ivo H. M. van Stokkum
examineFit, fitModel, opt-class, specopt-class