R/getDiffThetaChange.R

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

"getDiffThetaChange" <-
  function(th, mod) {
    modellist <- mod@modellist
    parorder <- mod@parorderchange
    diffchange <- mod@modeldiffs$change
    for (diffs in diffchange) {
      d <- diffs$dataset[1]
      if (diffs$what %in% slotNames(theta())) {
        fixedpar <- modellist[[d]]@fvecind[[
          which(attributes(modellist[[d]]@fvecind)$names
          == diffs$what)
        ]]
        ppar <- modellist[[d]]@pvecind[[
          which(attributes(modellist[[d]]@pvecind)$names
          == diffs$what)
        ]]
        removepar <- sort(unique(append(fixedpar, ppar)))
        parapp <- if (length(removepar) != 0) {
          unlist(slot(
            modellist[[d]],
            diffs$what
          ))[-removepar]
        } else {
          unlist(slot(
            modellist[[d]],
            diffs$what
          ))
        }
        if (length(parapp) != 0) {
          ind <- (length(th) + 1):(length(th) + length(parapp))
        } else {
          ind <- vector()
        }
        parorder[[length(parorder) + 1]] <- list(
          name = diffs$what,
          ind = ind, rm = removepar, dataset = diffs$dataset
        )

        if (diffs$what %in% modellist[[d]]@positivepar) {
          parapp <- log(parapp)
        } else {
          if (length(modellist[[d]]@clinde[[diffs$what]]) > 0) {
            for (i in 1:length(modellist[[d]]@clinde[[diffs$what]])) {
              parapp <- log(parapp[i])
            }
          }
          if (length(modellist[[d]]@chinde[[diffs$what]]) > 0) {
            for (i in 1:length(modellist[[d]]@chinde[[diffs$what]])) {
              parapp <- log(parapp[i])
            }
          }
        }
        th <- append(th, parapp)
      }
      if (diffs$what == "prelspec") {
        thA <- getPrelTheta(th, modellist, diffs, d, parorder)
        th <- thA$th
        parorder <- thA$parorder
      }
    }
    list(th = th, parorder = parorder)
  }