Class "kinopt" stores options for fitting and plotting kinetic
models in particular; this is a subclass of class opt
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.
Object of class "logical" that defaults to
FALSE; if TRUE, the data represent a FLIM experiment and
special plots are generated.
Object of class "logical" that defaults to
TRUE; if FALSE and a FLIM image is analyzed, the residuals
are not plotted as an image.
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.
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.
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.
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.
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).
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.
Katharine M. Mullen, Ivo H. M. van Stokkum
See opt-class for
the specification of fitting/plotting options that are not specific to the
class type.
examineFit, fitModel, opt-class, specopt-class