tests/kin_simple_visible_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("cp8b.txt")

##############################
## Look at the attributes of the data object
##############################

slotNames(mdDat)

##############################
## The times in the data
##############################

mdDat@x

##############################
## The number of timepoints in the data
##############################

mdDat@nt

##############################
## The wavelengths in the data
##############################

mdDat@x2

##############################
## The number of wavelengths in the data
##############################

mdDat@nl

##############################
## PREPROCESS PSI 1
## estimate the baseline from timepoints 1-9,
## and substract this baseline from data between wavelengths 1-256
##############################

mdDat <- preProcess(data = mdDat, baselinelambda = c(1, 9, 1, 256))

##############################
## PREPROCESS PSI 1
## Select wavelengths 1-235 for analysis
##############################

mdDat <- preProcess(data = mdDat, sel_lambda = c(1, 235))


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

model1 <- initModel(
  mod_type = "kin",
  kinpar = c(3.0, 0.5266452074, 0.8900437504E-01, 0.3096646687E-03),
  irfpar = c(-0.213412169, 0.66E-01),
  parmu = list(c(-0.4294245897, 0.663252115)),
  lambdac = 670,
  seqmod = TRUE,
  positivepar = c("kinpar"), weightpar = list(c(-16, -.1, NA, NA, .5)),
  title = "visible example",
  cohspec = list(type = "irf")
)

##############################
## FIT INITIAL MODEL
## plotting only every 20th trace
##############################

denRes <- fitModel(list(mdDat), list(model1),
  opt = kinopt(
    iter = 4, linrange = .2,
    makeps = "visible", xlab = "time (ps)",
    ylab = "wavelength", stderrclp = TRUE,
    plotkinspec = TRUE, kinspecerr = TRUE,
    selectedtraces = seq(1, 256, by = 20)
  )
)

##############################
## 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)
  }
}