R/fittingloop_bg.R

In danielcanueto/rDolphin: Reliable automatic profiling of 1D 1H NMR Spectra, with additional tools for analysis

fittingloop_bg = function(FeaturesMatrix, Xdata, Ydata, program_parameters) {

  residFun <-
    function(par, observed, xx,multiplicities,roof_effect,freq)
      observed - colSums(signal_fitting(par, xx,multiplicities,roof_effect,freq))

  # Loop to control if additional signals are incorporated, until a maximum of iterations specified bt fitting_maxiterrep.
  # If at the last fitting the improvement was lesser than 25% respective to the previous fitting,
  # iterrep becomes equal to fitting_maxiterrep and the loop is stooped
  lb = as.vector(t(FeaturesMatrix[, seq(1, 9, 2), drop = F]))
  ub = as.vector(t(FeaturesMatrix[, seq(2, 10, 2), drop = F]))
  multiplicities=FeaturesMatrix[,11]
  roof_effect=FeaturesMatrix[,12]

  s0 = lb + (ub - lb) * runif(length(ub))

  nls.out <-
    minpack.lm::nls.lm(
      par = s0,
      fn = residFun,
      observed = Ydata,
      xx = Xdata,
      multiplicities=multiplicities,
      roof_effect=roof_effect,
      lower = lb,
      upper = ub,
      freq=program_parameters$freq,
      control = minpack.lm::nls.lm.control(
        factor = program_parameters$factor,
        maxiter = program_parameters$nls_lm_maxiter,
        ftol = program_parameters$ftol,
        ptol = program_parameters$ptol
      )
    )
  dummy=list(BG_intensities = coef(nls.out)[which(seq(length(coef(nls.out)))%%5==1)],baseline=Ydata-nls.out$fvec)
  return(dummy)
}