modeldiffs |
list whose elements specify any dataset-specific
model differences.
- dscal
- list of lists specifying linear scaling relations between
datasets; each list has elements
to, from, value . The index of the
dataset to be scaled is given in to ; the index of the dataset on
which the scaling is to be based is given in from . The starting
value parameterizing the relationship is given as value . For
example, dscal = list(list(to=2,from=1,value=.457)) .
- free
- list of lists specifying individual
parameters to free for a given dataset. each sublist has
named elements
- what
- character string naming parameter type, e.g., "kinpar"
- ind
- vector or numeric of indices into parameter vector or list, e.g.,
c(2,3) or 4
- dataset
- dataset index in which parameter is to be freed
- start
- starting value for freed parameter
For example, free = list(
list(what = "irfpar", ind = 1, dataset = 2, start=-.1932),
list(what = "kinpar", ind = 5, dataset = 2, start=.0004),
list(what = "kinpar", ind = 4, dataset = 2, start= .0159)) .
- remove
- list of lists specifying individual
parameters to remove from
parameter groups for a given dataset. each sublist has
named elements
- what
- character string naming parameter type, e.g., "kinpar"
- dataset
- dataset index in which parameter group is to be removed
- ind
- vector or numeric of indices into parameter vector or list, e.g.,
c(2,3) or 4 where parameter should be removed
- add
- list of lists specifying individual
parameters to add to parameter groups for a given dataset. each sublist has
named elements
- what
- character string naming parameter type, e.g., "kinpar"
- dataset
- dataset index in which parameter group is to change
- start
- starting value for added parameter
- ind
- vector or numeric of indices into parameter vector or list, e.g.,
c(2,3) or 4 where parameter should be added.
- change
- list of lists specifying entire parameter groups to change
for a given dataset.
each sublist has named elements
- what
- character string naming parameter type, e.g., "kinpar"
- dataset
- dataset index in which parameter group is to change
- spec
- new specification that in initModel would follow "what",
e.g., for c(.1, .3) if what="kinpar"
- rel
- list of lists specifying parameters to relate between datasets
each sublist has named elements
- what1
- character string naming parameter type to be determined in
relation to some other parameter type , e.g., "kinpar"
- what2
- character string naming parameter type on which another
parameter type is to depend, e.g., "kinpar"
- ind1
- vector or numeric of indices into parameter vector or
list, e.g., c(2,3) or 4 of the dependent parameter.
- ind2
- vector or numeric of indices into parameter vector or
list, e.g., c(2,3) or 4 of the parameter on which another parameter will
depend
- dataset1
- dataset index of the dependent parameter
- dataset2
- dataset index of the parameter on which another parameter
will depend
- rel
- optional character string describing functional relationship
between parameters; defaults to "lin" for linear relationship
- start
- starting value or vector of values parameterizing
relationship between parameters
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opt |
list of options for fitting and display of results.
- iter
- integer number of iterations to optimize model parameters
- linrange
- 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
- plot
- Logical whose default value is TRUE; if FALSE then no plots or
output files are written
- superimpose
- vector of dataset indices whose results should be
superimposed in plots of traces
- selectedtraces
- vector of
x indices for which traces are
desired under a kinetic model
- notraces
- if length is non-zero, do not plot traces
- plotkinspec
- plot the spectra associated with the kinetics (leaving out
the coherent artifact/scatter)
- breakdown
- vector of time indices for which the breakdown of
contributions to the fit per-component is desired.
- xlabel
- character string label for x-axis, e.g.,
"nanoseconds"
or "picoseconds"
- ylabel
- character string label for y-axis, e.g.,
"wavelength"
- title
- character string title for plots
- makeps
- character string 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
- writefit
- logical, if true then fit is written to a txt file; row
and column labels are
x and x2
- writecon
- logical, if true then concentrations are
written to a txt file; row labels are
x
- writespec
- logical, if true then spectra are
written to a txt file; row labels are
x2
- writenormspec
- logical, if true then normalized spectra are
written to a txt file; row labels are
x2
- FLIM
- list; if present FLIM plotting options used
- paropt
- list of graphical parameters in format
par(...)
to apply to plots. Defaults to par(omi = tit,
mgp = c(2, 1, 0), mai = c(0.5, 0.5, 0.5, 0.25), mar=c(3,3,1,1)) ,
where tit = c(0, 0, 1, 0) if a title is specified in the call to
initModel , and tit = c(0, 0, 0, 0) otherwise.
- divrel
- if length is non-zero, 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.
- nospectra
- if length is non-zero, do not generate plots of data
and fit under a spectral model
- selectedspectra
- vector of
x2 indices for which plots of
spectra are and model fit are desired under a spectral model
- residplot
- if length is non-zero, generate a plot of residuals in a
separate window.
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