R/simndecay_gen.R

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

"simndecay_gen" <-
  function(kinpar, tmax, deltat, specpar = vector(), lmin, lmax, deltal,
           sigma, irf = FALSE, irfpar = vector(), seqmod = FALSE, dispmu
           = FALSE, nocolsums = FALSE,
           disptau = FALSE, parmu = list(), partau = vector(), lambdac = 0,
           fullk = FALSE, kmat = matrix(), jvec = vector(), specfun = "gaus",
           nupow = 1, irffun = "gaus", kinscal = vector(),
           lightregimespec = list(),
           specdisp = FALSE, specdisppar = list(), parmufunc = "exp",
           specdispindex = list(), amplitudes = vector(), specref = 0,
           fixedkmat = FALSE) {
    x <- seq(0, tmax, deltat)
    nt <- length(x)
    ncomp <- length(kinpar)
    x2 <- seq(lmin, lmax, deltal)
    nl <- length(x2)

    if (specdisp) {
      ## store all the spectra; could do it otherwise if mem. is an issue
      EList <- list()
      for (i in 1:nt) {
        sp <- specparF(
          specpar = specpar,
          xi = x[i],
          i = i, specref = specref,
          specdispindex = specdispindex,
          specdisppar = specdisppar,
          parmufunc = parmufunc
        )
        EList[[i]] <- calcEhiergaus(sp, x2, nupow)
      }
    } else {
      E2 <- calcEhiergaus(specpar, x2, nupow)
    }

    if (!(dispmu || disptau)) {
      C2 <- compModel(
        k = kinpar, x = x, irfpar = irfpar, irf = irf,
        seqmod = seqmod, fullk = fullk, kmat = kmat,
        jvec = jvec, amplitudes = amplitudes,
        lightregimespec = lightregimespec,
        nocolsums = nocolsums, kinscal = kinscal,
        fixedkmat = fixedkmat
      )
      if (specdisp) {
        psisim <- matrix(nrow = nt, ncol = nl)
        E2 <- EList[[1]]
        for (i in 1:nt) {
          psisim[i, ] <- t(as.matrix(C2[i, ])) %*% t(EList[[i]])
        }
      } else {
        psisim <- C2 %*% t(E2)
      }
    } else {
      psisim <- matrix(nrow = nt, ncol = nl)
      for (i in 1:nl) {
        irfvec <- irfparF(
          irfpar, lambdac, x2[i], i, dispmu,
          parmu, disptau, partau, "", "", "gaus"
        )

        C2 <- compModel(
          k = kinpar, x = x, irfpar = irfpar, irf = irf,
          seqmod = seqmod, fullk = fullk, kmat = kmat,
          jvec = jvec, amplitudes = amplitudes,
          lightregimespec = lightregimespec,
          nocolsums = nocolsums, kinscal = kinscal,
          fixedkmat = fixedkmat
        )
        psisim[, i] <- C2 %*% cbind(E2[i, ])
      }
    }
    dim(psisim) <- c(nt * nl, 1)
    psi.df <- psisim + sigma * rnorm(nt * nl)
    dim(psi.df) <- c(nt, nl)

    kin(
      psi.df = psi.df, x = x, nt = nt, x2 = x2, nl = nl, C2 = C2,
      E2 = E2, kinpar = kinpar, specpar = specpar,
      seqmod = seqmod, irf = irf, irfpar = irfpar,
      dispmu = dispmu, disptau = disptau, parmu = parmu, partau = partau,
      lambdac = lambdac, simdata = TRUE, fullk = fullk, kmat = kmat,
      jvec = jvec, fixedkmat = fixedkmat
    )
  }