kinopt-class {TIMP} | R Documentation |
Class "kinopt" stores options for fitting and plotting kinetic
models in particular; this is a subclass of class opt
See opt-class
for
the specification of fitting/plotting options that are not specific to the
class type.
Objects can be created by calls of the form new("kinopt", ...)
or
kinopt(...)
notraces
:"logical"
that defaults
to FALSE
; if TRUE
, do not plot tracesselectedtraces
:"vector"
containing
x
indices for which plots of
traces are desired under a kinetic model breakdown
:"list"
with the
following elements:
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
modelled.
plot
are compared to x2
values
for near-equality. The default is defined as
abs(x2[1] - x2[2])/100
. x2
value at a value in
plot
."logical"
that defaults to
FALSE
; if TRUE
, the data represent a FLIM experiment and
special plots are generated. "logical"
that defaults to
TRUE
; if FALSE
and a FLIM image is analyzed, the residuals
are not plotted as an image."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."logical"
that defaults to
FALSE
; if TRUE
, make a plot of the spectra associated with
the kinetic components as well as the lifetime estimates. "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.
"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.
"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
:"logical"
defaults to
FALSE
; if TRUE
adding imageplots of pulsefolower amplitudes in summary plot (only with FLIM plots)."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
examineFit
, fitModel
, opt-class
, specopt-class