initModel: Defines the model to be used in analysis.

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

Defines the model to be used in analysis.

Description

Allows definition of a model of class "dat" to be used in analysis. The arguments specify the model.

Usage

initModel(...)

Arguments

...	specify the model class via the character string e.g., kin-class or spec and any of the slots associated with that model type (which is a subclass of class dat, so that all slots in dat may also be specified), e.g., mod_type = "kin" will initialize a model with class kin, for a kinetic model.

Details

For examples, see the help files for dat-class and fitModel

Value

an object of class dat with the sub-class given by the value of the mod_type input.

Author(s)

Katharine M. Mullen, Ivo H. M. van Stokkum

See Also

dat-class, kin-class, spec-class, fitModel

Examples

##############################
## READ IN PSI 1
##############################

data(denS4)

##############################
## PREPROCESS PSI 1
##############################

denS4<-preProcess(data = denS4, scalx2 = c(3.78, 643.5))

##############################
## READ IN PSI 2
##############################

data(denS5)

##############################
## PREPROCESS PSI 2
##############################

denS5<-preProcess(data = denS5, scalx2 = c(3.78, 643.5))

##############################
## DEFINE INITIAL MODEL
##############################

model1<- initModel(mod_type = "kin",
kinpar= c(7.9, 1.08, 0.129, .0225, .00156) ,
irfpar=c( -.1018, 0.0434),
disptau=FALSE, dispmu=TRUE, parmu = list(c(.230)),
lambdac = 650,
seqmod=TRUE,
positivepar=c("kinpar"),
title="S4",
cohspec = list( type = "irf"))



##############################
## FIT INITIAL MODEL
##############################

denRes1 <- fitModel(data=list(denS4, denS5), list(model1),
opt=kinopt(iter=5, divdrel = TRUE, linrange = .2,
makeps = "den1", selectedtraces = c(1,5,10), plotkinspec =TRUE,
output="pdf", xlab = "time (ps)", ylab = "wavelength"))

##############################
## REFINE INITIAL MODEL, RE-FIT
## adding some per-dataset parameters
##############################

denRes2 <- fitModel(data = list(denS4, denS5), modspec = list(model1),
modeldiffs = list(dscal = list(list(to=2,from=1,value=.457)),
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)
)),
opt=kinopt(iter=5, divdrel = TRUE, linrange = .2,
xlab = "time (ps)", ylab = "wavelength", output="pdf",
makeps = "den2", selectedtraces = c(1,5,10)))

##############################
## REFINE MODEL FURTHER AS NEW MODEL OBJECT
##############################

model2 <- initModel(mod_type = "kin",
kinpar= c(7.9, 1.08, 0.129, .0225, .00156),
irfpar=c( -.1018, 0.0434),
parmu = list(c(.230)),
lambdac = 650,
positivepar=c("kinpar", "coh"),
cohspec = list( type = "seq", start = c(8000, 1800)))

##############################
## FIT NEW MODEL OBJECT
##############################

denRes3 <- fitModel(data = list(denS4, denS5), list(model2),
modeldiffs = list(dscal = list(list(to=2,from=1,value=.457)),
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)
)),
opt=kinopt(iter=5, divdrel = TRUE, linrange = .2,
makeps = "den3", selectedtraces = c(1,5,10), plotkinspec =TRUE,
stderrclp = TRUE, kinspecerr=TRUE, output="pdf",
xlab = "time (ps)", ylab = "wavelength",
breakdown = list(plot=c(643.50, 658.62, 677.5))))

 # end donttest

##############################
## CLEANUP GENERATED FILES
##############################
# This removes the files that were generated in this example
# (do not run this code if you wish to inspect the output)
file_list_cleanup = c('den1_paramEst.txt', 'den2_paramEst.txt', 'den3_paramEst.txt',
  Sys.glob("*paramEst.txt"), Sys.glob("*.ps"), Sys.glob("Rplots*.pdf"))

# Iterate over the files and delete them if they exist
for (f in file_list_cleanup) {
  if (file.exists(f)) {
    unlink(f)
  }
}

TIMP documentation built on Dec. 28, 2022, 3:06 a.m.