Class "opt" stores options for fitting and plotting applicable to all model types
Objects can be created by calls of the form new("opt", ...)
or
opt(...)
.
algorithm
:Object of class "character"
that defaults to
algorithm="nls"
, so that the function nls
is used to
optimize nonlinear parameters under least squares criteria.
Other options are
nls.lm
:optimize nonlinear parameters under least
squares criteria using nls.lm
optim
:optimize nonlinear parameters under poisson
regression criteria with the Nelder-Mead algorithm in
optim
; if this option is used then it MUST be used in
conjunction with nnls=TRUE
. Currently, it must also be
used with stderrclp=FALSE
.
nnls
:Object of class "logical"
that defaults to
FALSE
. If nnls=TRUE
,
constrain the conditionally linear parameters
to nonnegativity via a nonnegative least squares algorithm as
implemented via the function nnls
from the package by the same
name.
writecon
:Object of class "logical"
that defaults to
FALSE
; if true then
concentrations are written to a txt file; row labels are x
writespec
:Object of class "logical"
that defaults to
FALSE
; if TRUE
then
spectra are written to a txt file; row labels are x2
writenormspec
:Object of class "logical"
that
defaults to FALSE
; if TRUE
then normalized spectra are
written to a txt file; row labels are x2
writefit
:Object of class
"logical"
that defaults to FALSE
; if TRUE
then fit
is written to a txt file; row and column labels are x
and
x2
writeclperr
:Object of class "logical"
that defaults to
FALSE; if true then
the error bars for clp are written to a txt file. This option is only
sensible with stderrclp=TRUE
.
output
:Object of class
"character"
that defaults to "ps"
, which means that
plots written to file are postscript. Alternatively, specify
output = "pdf"
, and plots are written as pdf files
addfilename
:Object of class
"logical"
that, for each data file, tries to add the
filename to plots associated with output for that data.
residplot
:Object of class "logical"
defaults to
FALSE
; if TRUE
generate a plot of residuals in a
separate window.
adddataimage
:Object of class "logical"
defaults to
FALSE
; if TRUE
adding imageplot of data in summary plot.
plot
:Object of class "logical"
that defaults to
TRUE
; if FALSE
then do not write output in the form of
plots and other windows to the screen.
divdrel
:Object of class "logical"
that defaults to
FALSE
; if TRUE
, plot traces and concentration
profiles divided by the dataset scaling parameters where they apply; this
allows for the fit of datasets having different intensities on the same
scale.
plotkinspec
:Object of class "logical"
that defaults
to FALSE
; if TRUE
, generates a separate plot of the spectra
associated with the components that are not a part of a coherent
artifact/scatter model.
superimpose
:Object of class "vector"
containing
dataset indices whose results should be superimposed in plots
xlab
:Object of class "character"
containing
label for x-axis, e.g., "nanoseconds"
or "picoseconds"
ylab
:Object of class "character"
containing label
for y-axis, e.g., "wavelength"
title
:Object of class "character"
containing title
to write at the top of plots.
makeps
:Object of class "character"
containing
prefix to plot files written to postscript;
if present postscript will be written. Note that this string is also
used as the preffix of txt output files
linrange
:Object of class "numeric"
giving linear
range of time axis for plotting; time will be plotted linearly from
-linrange to linrange and plotted on a logarithmic (base 10) axis elsewhere
summaryplotrow
:Object of class "numeric"
giving
number of rows in summary plot; defaults to 4
summaryplotcol
:Object of class "numeric"
giving
number of columns in summary plot; defaults to 4
iter
:Object of class "numeric"
giving
number of iterations to optimize model parameters; if
nls=FALSE
so that the Levenberg-Marquardt algorithm is
applied, then iter
is interpreted as the
maximum number of residual function evaluations (see the help
page of the function nls.lm
for details)
paropt
:Object of class "list"
of graphical parameters in format par(...)
to apply to plots.
stderrclp
:Object of class "logical"
that defaults
to FALSE
; if TRUE
, estimates of the standard error of
conditionally linear parameters are made
addest
:Object of class "vector"
containing
character strings of which parameter estimates should be added to the
summary plot, e.g., addest = c("kinpar", "irfpar")
Object of class "logical"
that defaults to
FALSE
; if TRUE
, add standard error estimates to the clp
a plot generated with kinspecest=TRUE
or
plotkinspec=TRUE
. This option can only be
used if the estimates were generated during fitting via the option
stderrclp=TRUE
Object of class "vector"
that defaults to
vector()
; if changed, it should specify the desired x-limits of
the plot of clp
Object of class "vector"
that defaults to
vector()
; if changed, it should specify the desired y-limits of
the plot of clp. 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 lifetimes.
Object of class "vector"
that defaults to
vector()
; if changed, the first value should specify a vector to
add to the y-limits of the plot of clp
Object of class "logical"
that defaults to
FALSE
; if TRUE
, then the line-type for clp is the same
for all datasets
Object of class "logical"
that defaults to
FALSE
; if TRUE
, use spline instead of lines between
the points representing estimated clp
Object of class "logical"
that defaults to
TRUE
; if TRUE
, add points representing the actual estimates
for clp to plots of the curves representing smoothed clp
Object of class "numeric"
that defaults to
50
; represents the number of segments used in a spline-based
representation of clp
Object of class "logical"
that defaults
to FALSE
; determines whether a B-spline based representation of
clp is used (when specinterpol=TRUE
) or a piecewise polynomial
representation
Object of class "logical"
that determines whether
clp are normalized in plots
Object of class "logical"
that defaults to
FALSE
; if TRUE
, a spline-based representation of clp
is written to ASCII files
Object of class "character"
that defaults to
"default"
and determines the algorithm used by nls
, if
nls
is used in optimization. See help(nls)
for other
possibilities, such as "port"
, which is more stable with
respect to starting values but requires more time.
Object of class "numeric"
if given, sets the line
type of the fit in plots of the fit/data; see lty
in
help(par)
for options.
Object of class "numeric"
if given, sets the line
type of the data in plots of the fit/data; see lty
in
help(par)
for options.
Object of class "vector"
if given, sets the color
of the fit corresponding to each dataset
in plots of the fit/data; see col
in
help(par)
for options. If given
length(colfit)
must be equal to
the number of datasets in the analysis
Object of class "vector"
if given, sets the color
of the data for each dataset
in plots of the fit/data; see col
in
help(par)
for options. If given,
length(coldata)
must be equal to
the number of datasets in the analysis
Katharine M. Mullen, Ivo H. M. van Stokkum
See kinopt-class
, specopt-class
and
massopt-class
for
the specification of fitting/plotting options that are specific to the
class type.
kinopt-class
, specopt-class