tests/kin_simple_ir_script.R

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

##############################
## Dataset and model of
## Mariangela di Donato.
##############################

##############################
## load TIMP
##############################

require(TIMP)

##############################
## READ IN DATA
##############################

mdDat <- readData("cp432704.txt")

##############################
## PREPROCESS PSI 1
## estimate the baseline from timepoints 1-5,
## and substract this baseline from data between wavelengths 1-32
##############################

mdDat <- preProcess(data = mdDat, baselinelambda = c(1, 5, 1, 32))

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

model1 <- initModel(
  mod_type = "kin",
  kinpar = c(1.0, 0.01, 0.005), irfpar = c(.003, .095),
  parmu = list(c(.073)), lambdac = 1670,
  seqmod = TRUE,
  positivepar = c("kinpar"), weightpar = list(c(-16, -.1, NA, NA, .1)),
  makeps = "MARI", title = "MARI",
  cohspec = list(type = "irf")
)

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

denRes <- fitModel(list(mdDat), list(model1),
  opt = kinopt(
    iter = 5, linrange = .2,
    makeps = "MARI", xlab = "time (ps)",
    ylab = "wavelength", plotkinspec = TRUE
  )
)

##############################
## 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(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)
  }
}