R/surrogate-iterated-aaft.R

Defines functions iaaft_surrogate

Documented in iaaft_surrogate

#' Generate an iterated amplitude-adjusted Fourier transform surrogate.
#' Constrained to the values of the original time series.
#'
#' @param series The series for which to generate a surrogate.
#' @param n.max.iter The maximum number of refinement.
#' @return An iaaft representation of the original series, sticking to
#'   the original values of the series (but otherwise shuffled) and
#'   preserving the autocorrelation function of the original series.
#' @export iaaft_surrogate
#'
iaaft_surrogate <- function(series, n.max.iter = 150) {
  if (!is_valid_input(series)) {
    rlang::abort("Surrogate generation failed. Input series is not valid!")
  }

  n <- length(series)

  # Fourier transform of the original series
  original_fft <- stats::fft(series)

  # Amplitudes of the original Fourier transform
  original_fft_amplitudes <- Mod(original_fft)

  # Sample a Gaussian vector and sort it
  gaussian <- sort(stats::rnorm(n, 0, 2), index.return = T)$ix

  # Sort the original series according to the sorted Gaussian. After a number
  # of iterations, this will be our final surrogate series.
  series.randsorted <- series[gaussian]

  # Iterate until autocorrelation functions match sufficiently.
  iteration <- 0
  convergence.achieved <- FALSE

  tolerance <- 0.00001

  # Compute root mean square difference between original and randomly sorted
  # series
  acf.diff.old <- sqrt(sum((stats::acf(series, n - 1, plot = F)$acf -
                  stats::acf(series.randsorted, n - 1, plot = F)$acf) ^ 2))


  while (!convergence.achieved && iteration <= n.max.iter) {
    series.randsorted.fft <- stats::fft(series.randsorted)

    # Extract the phases from the Fourier transform of the randomly
    # sorted series.
    randomised.phases <- Arg(series.randsorted.fft)

    # New spectrum preserving original amplitudes but using the randomised
    # phases.
    new_fft <- original_fft_amplitudes * exp(randomised.phases * 1i)

    # fft with inverse = T returns unnormalised values, so normalise by n
    surrogate <- Re(stats::fft(new_fft, inverse = T)) / n # Sample the real part

    surrogate[sort(surrogate, index.return = T)$ix] <- sort(series)

    series.randsorted <- surrogate

    # Check for convergence
    acf.diff.new <- sqrt(sum((stats::acf(series, n - 1, plot = F)$acf -
                    stats::acf(surrogate, n - 1, plot = F)$acf)^2))

    if (abs(acf.diff.old - acf.diff.new) < tolerance) {
        #cat("\nConvergence achieved after ", iteration, " iterations.\n")
        convergence.achieved <- T
    } else {
        acf.diff.old <- acf.diff.new
    }
    iteration <- iteration + 1
  }
  return(surrogate)
}
kahaaga/tstools documentation built on Nov. 30, 2017, 7:24 a.m.