R/fillK.R

In glotaran/TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

"fillK" <- function(theta, kinscal, kmat, fixedkmat, kinscalspecial,
                    kinscalspecialspec, nocolsums = FALSE) {
  # fillK
  if (!fixedkmat) {
    if (length(kinscalspecialspec) > 0) {
      special <- TRUE
    } else {
      special <- FALSE
    }
    ## kmat is 3d array with elements kmat[i,j,]
    ## <- c(thetaindex, theta scal index)
    dimk <- nrow(kmat) ## kmat is square
    reskmat <- matrix(0, nrow = dimk, ncol = dimk)
    for (i in 1:dimk) {
      for (j in 1:dimk) {
        if (!(special || nocolsums)) {
          if (i == j) {
            pl <- -1
          } else {
            pl <- 1
          }
        } else {
          pl <- 1
        }

        if (!special) { ## k is (possibly) linearly dep. on scaling
          if (kmat[i, j, 1] != 0 && kmat[i, j, 2] != 0) {
            ## use scaling and theta
            reskmat[i, j] <- pl * theta[kmat[i, j, 1]] *
              kinscal[kmat[i, j, 2]]
          }
          if (kmat[i, j, 1] != 0 && kmat[i, j, 2] == 0) {
            ## use theta
            reskmat[i, j] <- pl * theta[kmat[i, j, 1]]
          }
          if (kmat[i, j, 1] == 0 && kmat[i, j, 2] != 0) {
            ## use scaling
            reskmat[i, j] <- pl * kinscal[kmat[i, j, 2]]
          }
        } else { ## have a function to describe k
          if (kmat[i, j, 2] != 0) {
            reskmat[i, j] <- applyKinScalSpecialFun(
              ind = kmat[i, j, 2],
              theta = theta,
              kinscalspecial, kinscalspecialspec
            )
          }
        }
      }
    }
    if (!(special || nocolsums)) {
      for (i in 1:dimk) {
        for (j in 1:dimk) {
          if (i != j) {
            reskmat[j, j] <- reskmat[j, j] - reskmat[i, j]
          }
        }
      }
    }
  } else {
    diag(kmat) <- -colSums(kmat)
    reskmat <- kmat
  }
  reskmat
}