R/init.opt.R

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

    setClass("opt", 
             representation(notraces = "logical",
                            residtraces = "logical",
                            selectedtraces = "vector",
                            writecon = "logical", 
                            writespec = "logical", 
                            writenormspec = "logical", 
                            writefit = "logical", 
                            writefitivo = "logical",
                            writedata = "logical",
                            writeclperr = "logical",
                            residplot = "logical", 
                            plot = "logical",
                            minFactor = "numeric", 
                            output = "character",
                            nnls = "logical", 
                            divdrel = "logical", 
                            noplotest = "logical",
                            plotkinspec = "logical",
                            algorithm = "character",
                            superimpose = "vector",
                            xlab = "character",
                            ylab = "character",
                            title = "character",
                            makeps = "character",
                            linrange = "numeric",
                            summaryplotrow = "numeric",
                            summaryplotcol = "numeric",
                            iter = "numeric",
                            stderrclp = "logical",
                            trilinear = "logical",
                            getStartTri = "logical",
                            triStart = "list",
                            paropt="list", 
                            addfilename = "logical",
                            addest="vector", 
                            adddataimage = "logical",
                            kinspecerr = "logical",
                            xlimspec = "vector",
                            ylimspec = "vector",
                            ylimspecplus = "vector",
                            xlim = "vector",
                            specinterpol = "logical",
                            specinterpolpoints = "logical",
                            specinterpolseg = "numeric",
                            specinterpolbspline = "logical",
                            samespecline = "logical",
                            normspec = "logical",
                            writespecinterpol = "logical", 
                            nnlscrit = "list",
                            nlsalgorithm = "character",
                            sumnls = "logical",
                            colfit = "vector",
                            coldata = "vector",
                            ltyfit = "numeric",
                            ltydata = "numeric",
                            optimmethod = "character",
                            parscale = "vector",
                            maxfev = "numeric",
                            imagepal = "vector"
			), 
        prototype = list(
                        writecon = FALSE, 
			writespec = FALSE,
			writenormspec = FALSE,
			writefit = FALSE,
                        writefitivo = FALSE,
			writeclperr = FALSE,
                        writedata = FALSE, 
                        algorithm = "nls",
                        residtraces = FALSE,
			noplotest = FALSE,
                        residplot = FALSE, 
			plotkinspec = FALSE,
                        minFactor = 1/1024,
                        plot = TRUE,
                        trilinear = FALSE,
          getStartTri = TRUE,
          triStart = list(),
          addfilename = FALSE,
	  adddataimage = FALSE,
          divdrel = TRUE, 
          output = "ps", 
          nnls = FALSE,
          superimpose = vector(),
          paropt = list(),
          title = "",
          makeps = "",
          stderrclp = FALSE, 
          summaryplotrow = 3, 
          summaryplotcol = 4,
          linrange = 1,
          iter = 1, 
          addest=vector(), 
          kinspecerr = FALSE,
          ylimspecplus = vector(), 
          xlimspec = vector(),
          ylimspec = vector(),
          xlim = vector(),
          specinterpol = FALSE,
          specinterpolpoints = TRUE, 
          specinterpolseg = 50,
          specinterpolbspline = FALSE,
          normspec = FALSE,
          writespecinterpol = FALSE, 
          samespecline = FALSE,
          nnlscrit = list(),
          nlsalgorithm = "default",
          sumnls = TRUE,
          notraces = FALSE,
          selectedtraces = vector(),
          colfit = vector(),
          coldata = vector(),
          ltyfit = numeric(),
          ltydata = numeric(),
          optimmethod = "Nelder-Mead",
          parscale = vector(),
          maxfev= 900,
          imagepal = vector()
          ))

setClass("kinopt", representation("opt",
                                  breakdown = "list",
                                  FLIM = "logical", 
                                  FLIMresidimag = "logical",
                                  noFLIMsummary = "logical",
                                  writerawcon = "logical",
                                  plotcohcolspec = "logical", 
                                  kinspecest = "logical",
                                  writeplaincon = "list",
                                  plotpulsefol = "logical",
                                  ylimcomp = "vector"),
         prototype = list( 
           breakdown = list(),
           writerawcon = FALSE,
           plotcohcolspec = TRUE,
           addest = c("kinpar"),
           FLIM = FALSE,	
           FLIMresidimag = TRUE, 
           noFLIMsummary = FALSE,
           paropt =  par(mgp = c(1.5, 1, 0), 
             mai = c(0.5, 0.6, .5, 0.5),mar=c(3,3,4,1)),
           xlab = "time",
           ylab = "wavelength",
           kinspecest = FALSE,
           writeplaincon = list(),
           plotpulsefol = FALSE,
           ylimcomp = vector()
          ))

setClass("massopt", representation("kinopt", axis.by = "numeric",
        scale.concen = "logical", nummaxtraces = "numeric"), prototype
        = list(normspec = TRUE, axis.by = 30, scale.concen = TRUE,
        nummaxtraces = 0) )

setClass("specopt", representation("opt", nospectra = "logical",
			   selectedspectra = "vector"), prototype =
			   list( nospectra = FALSE, selectedspectra =
			   vector(), xlab = "wavelength", ylab =
			   "time"))