R/getCoh.R

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

"getCoh" <-
  function(model) {
    ## type is "irf", "freeirfdisp" "irfmulti" "seq", "mix" or "xpm"
    numcohcol <- 0
    if (model@cohspec$type == "irf" ||
      model@cohspec$type == "freeirfdisp") {
      numcohcol <- 1
      if (length(model@nl) == 0) {
        model@ncolc <- array(model@ncomp + 1, 1)
      } else {
        model@ncolc <- array(model@ncomp + 1, model@nl)
      }
    }
    if (model@cohspec$type == "seq") {
      numcohcol <- length(model@cohspec$start)
      model@coh <- model@cohspec$start
      if (length(model@nl) == 0) {
        model@ncolc <-
          array(model@ncomp + length(model@coh), 1)
      } else {
        model@ncolc <-
          array(model@ncomp + length(model@coh), model@nl)
      }
    }
    if (model@cohspec$type == "xpm" || model@cohspec$type == "XPM") {
      if (length(model@cohspec$start) > 0 && length(model@coh) == 0) {
        model@coh <- model@cohspec$start
      }
      numosccol <- floor(length(model@coh) / 3)

      if (length(model@nl) == 0) {
        model@ncolc <-
          array(model@ncomp + numosccol, 1)
      } else {
        model@ncolc <-
          array(model@ncomp + numosccol, model@nl)
      }
    }


    if (model@cohspec$type == "irfmulti") {
      if (length(model@nl) == 0) {
        model@ncolc <- array(
          model@ncomp + model@cohspec$numdatasets,
          1
        )
      } else {
        model@ncolc <- array(
          model@ncomp + model@cohspec$numdatasets,
          model@nl
        )
      }
      numcohcol <- model@cohspec$numdatasets
    }
    if (model@cohspec$type == "mix") {
      numcohcol <- length(model@cohspec$start) + 1
      model@coh <- model@cohspec$start
      if (length(model@nl) == 0) {
        model@ncolc <- array(
          model@ncomp + length(model@coh) + 1,
          1
        )
      } else {
        model@ncolc <- array(
          model@ncomp + length(model@coh) + 1,
          model@nl
        )
      }
    }
    if (length(model@anispec$rammanest) != 0) {
      if (model@anispec$rammanest) {
        numcohcol <- numcohcol + 1
        model@ncolc <- model@ncolc + 1
      }
    } else {
      model@anispec$rammanest <- FALSE
    }
    if (numcohcol > 0) {
      model@cohcol <- (model@ncolc[1] - numcohcol + 1):model@ncolc[1]
    }
    model@ncomp <- max(model@ncolc)
    model
  }