R/init.dat.R

In TIMP: Fitting Separable Nonlinear Models in Spectroscopy and Microscopy

setClass("dat", representation(
  psi.df = "matrix", psi.weight = "matrix",
  x = "vector", nt = "integer", x2 = "vector", nl = "integer",
  C2 = "matrix", E2 = "matrix", sigma = "numeric",
  mod_type = "character", parnames = "vector", dummy = "vector",
  simdata = "logical", weightpar = "list",
  weight = "logical", weightM = "matrix", weightsmooth = "list",
  fixed = "list", clp0 = "list", makeps = "character",
  clpequspec = "list", lclp0 = "logical", lclpequ = "logical",
  title = "character", mhist = "list", datCall = "list",
  dscalspec = "list", mvecind = "vector", dscal = "list",
  drel = "vector", clpequ = "vector", scalx = "numeric",
  prel = "vector", prelspec = "list", fvecind = "vector",
  pvecind = "vector", nvecind = "vector",
  iter = "numeric", free = "list",
  clpCon = "list", ncomp = "numeric", clpdep = "logical",
  inten = "matrix", positivepar = "vector", constrained = "list",
  clinde = "list", chinde = "list", highcon = "vector",
  lowcon = "vector", datafile = "character", getX = "logical",
  clpType = "character", clpequspecBD = "list", compnames = "vector",
  getXsuper = "logical", usecompnames0 = "logical",
  usecompnamesequ = "logical", autoclp0 = "list", cohcol = "numeric",
  weightList = "list", outMat = "matrix", satMat = "matrix",
  lscalpar = "logical", thetascal = "vector"
),
prototype = list(
  psi.df = matrix(), psi.weight = matrix(),
  x = vector(), nt = integer(), x2 = vector(), nl = integer(),
  C2 = matrix(), E2 = matrix(), sigma = numeric(),
  mod_type = character(), simdata = logical(),
  weightpar = list(), weight = FALSE, weightM = matrix(),
  weightsmooth = list(), fixed = list(), clp0 = list(),
  clpequspec = list(), clpCon = list(), lclp0 = logical(),
  lclpequ = logical(), makeps = character(), title = character(),
  mhist = list(), datCall = list(), nvecind = vector(),
  dscal = list(), drel = vector(), mvecind = vector(),
  scalx = 1, prel = vector(), prelspec = list(), fvecind = vector(),
  pvecind = vector(), clpequ = vector(), free = list(),
  iter = 1, ncomp = numeric(), clpdep = logical(), inten = matrix(),
  parnames = vector(), dummy = vector(), positivepar = vector(), constrained = list(),
  clinde = list(), chinde = list(), highcon = vector(),
  lowcon = vector(), datafile = "", getX = FALSE,
  clpType = "", clpequspecBD = list(), compnames = vector(),
  getXsuper = FALSE, usecompnames0 = FALSE,
  usecompnamesequ = FALSE, autoclp0 = list(), cohcol = 0,
  weightList = list(), outMat = matrix(), satMat = matrix(),
  lscalpar = FALSE, thetascal = vector()
)
)

setClass("kin", representation("dat",
  kinpar = "vector", specpar =
    "list", seqmod = "logical", irf = "logical", mirf = "logical",
  reftau = "numeric", measured_irf = "vector", convalg =
    "numeric", irffun = "character", irfpar = "vector", cohirf = "vector",
  dispmu = "logical", dispmufun = "character", anipar = "vector",
  parmu = "list", disptau = "logical", disptaufun = "character", partau =
    "vector", fullk = "logical", kmat = "array", jvec = "vector",
  anispec = "list", ncolc = "vector",
  kinscal = "vector", kmatfit = "array", cohspec = "list", coh = "vector",
  oscspec = "list", oscpar = "vector",
  wavedep = "logical", lambdac = "numeric", speckin2 = "list",
  usekin2 = "logical", kinpar2 = "vector",
  kin2scal = "vector", amplitudes = "vector", streakT = "numeric",
  streak = "logical", doublegaus = "logical", multiplegaus = "logical", fixedkmat = "logical",
  kinscalspecialspec = "list", kinscalspecial = "list",
  lightregimespec = "list",
  numericalintegration = "logical", initialvals = "vector",
  reactantstoichiometrymatrix = "vector",
  stoichiometrymatrix = "vector"
),
prototype = list(
  kinpar = vector(), seqmod =
    TRUE, irf = FALSE, mirf = FALSE, measured_irf = vector(), convalg = 1,
  cohirf = vector(), irffun = "gaus", anispec = list(), irfpar =
    vector(), dispmu = FALSE, dispmufun = "poly", parmu = list(), anipar =
    vector(), disptaufun = "poly", reftau = 0, specpar = list(),
  partau = vector(), disptau = FALSE, fullk = FALSE,
  kmat = array(), jvec = vector(),
  ncolc = vector(), kinscal = vector(), kmatfit = array(),
  cohspec = list(), coh = vector(), oscspec = list(), oscpar = vector(), wavedep = logical(),
  lambdac = numeric(), speckin2 = list(), usekin2 = FALSE,
  kinpar2 = vector(), kin2scal = vector(), amplitudes = vector(),
  streakT = 0, streak = FALSE, doublegaus = FALSE, multiplegaus = FALSE, fixedkmat = FALSE,
  kinscalspecialspec = list(), kinscalspecial = list(),
  lightregimespec = list(), numericalintegration = FALSE,
  initialvals = vector(),
  reactantstoichiometrymatrix = vector(),
  stoichiometrymatrix = vector()
)
)

setClass("mass",
  representation("kin",
    peakpar = "list",
    amplitudes = "vector",
    peakfunct = "character",
    lzerofile = "character",
    extracomp = "logical",
    shift = "vector"
  ),
  prototype = list(
    peakpar = list(),
    peakfunct = "expmodgaus",
    lzerofile = "",
    amplitudes = vector(),
    getX = TRUE,
    extracomp = TRUE,
    shift = vector()
  )
)

setClass("spec", representation("dat",
  clpequ = "vector",
  specpar = "list", specfun = "character", specref = "numeric",
  specCon = "list", ncole = "vector", specdisp = "logical",
  specdisppar = "list", specdispindex = "vector", nupow = "numeric",
  timedep = "logical", parmufunc = "character"
),
prototype = list(
  specpar = list(), specfun = "gaus",
  specCon = list(), ncole = vector(), specdisp = FALSE,
  specdisppar = list(), specdispindex = vector(), specref =
    numeric(), nupow = 5, clpequ = vector(),
  timedep = FALSE, parmufunc = "poly"
)
)

setClass("amp", representation("dat", amps = "list"),
  prototype = list(amps = list(), clpdep = FALSE)
)