R/DFA.R

Defines functions estimate.dfa plot.dfa fluctuationFunction.dfa fluctuationFunction windowSizes.dfa windowSizes dfa

Documented in dfa estimate.dfa fluctuationFunction fluctuationFunction.dfa plot.dfa windowSizes windowSizes.dfa

#' Detrended Fluctuation Analysis
#' @description
#' Functions for performing Detrended Fluctuation Analysis (DFA), a widely used
#' technique for detecting long range correlations in time series. These 
#' functions are able to estimate several scaling exponents from the time series 
#' being analyzed. 
#' These scaling exponents  characterize short or long-term fluctuations, 
#' depending of the range used for regression (see  details).
#' @details The Detrended Fluctuation Analysis (DFA) has become a widely used
#' technique for detecting long range correlations in time series. The DFA 
#' procedure may be summarized as follows:
#' \enumerate{
#'  \item Integrate the time series to be analyzed. The time series resulting 
#'  from the  integration will be referred to as the profile.
#'  \item Divide the profile into N non-overlapping segments.
#'  \item  Calculate the local trend for each of the segments using least-square
#'  regression. Compute the total error for each ofi the segments.
#'  \item Compute the average of the total error over all segments and take its 
#'  root square. By repeating the previous steps for several segment sizes 
#'  (let's denote it by t), we obtain the so-called Fluctuation function 
#'  \eqn{F(t)}.
#'  \item  If the data presents long-range power law correlations:  
#'  \eqn{F(t) \sim t^\alpha}{F(t) proportional t^alpha} and we may estimate 
#'  using regression.
#'  \item  Usually, when plotting 
#'  \eqn{\log(F(t))\;Vs\;log(t)}{log(F(t)) Vs log(t)} 
#'  we may distinguish two linear regions.
#'  By regressing them separately, we obtain two scaling exponents, 
#'  \emph{\eqn{\alpha_1}{alpha1}} (characterizing short-term fluctuations) and 
#'  \emph{\eqn{\alpha_2}{alpha2}} (characterizing long-term fluctuations). 
#' }
#' Steps 1-4 are performed using the \emph{dfa} function. In order to obtain a 
#' estimate of some scaling exponent, the user must use the  \emph{estimate} 
#' function specifying the regression range (window sizes used to detrend the 
#' series).
#' @param time.series The original time series to be analyzed.
#' @param npoints The number of different window sizes that will be used to 
#' estimate the Fluctuation function in each zone.
#' @param window.size.range Range of values for the windows size that will be 
#' used to estimate the fluctuation function. Default: c(10,300).
#' @param do.plot logical value. If TRUE (default value), a plot of the 
#' Fluctuation function is shown.
#' @param ... Additional graphical parameters.
#' @return A \emph{dfa}  object.
#' @author Constantino A. Garcia
#' @examples
#' \dontrun{
#'  white.noise = rnorm(5000)
#' dfa.analysis = dfa(time.series = white.noise, npoints = 10, 
#'                  window.size.range=c(10,1000), do.plot=FALSE)
#' white.estimation = estimate(dfa.analysis,do.plot=TRUE)
#' cat("Theorical: 0.5---Estimated: ",white.estimation ,"\n")
#' 
#' 
#' library(fArma)
#' fgn = as.numeric(fArma::fgnSim(n = 2000, H = 0.75))
#' dfa.analysis = dfa(time.series = fgn, npoints = 30, 
#'                    window.size.range=c(10,1000), 
#'                    do.plot=FALSE)
#' fgn.estimation = estimate(dfa.analysis, do.plot = TRUE,
#'                           fit.col="blue",fit.lwd=2,fit.lty=2,
#'                           main="Fitting DFA to fGn")
#' cat("Theorical: 0.75---Estimated: ",fgn.estimation ,"\n")
#' 
#' 
#' fbm = as.numeric(fArma::fbmSim(n = 2000, H = 0.25))
#' dfa.analysis = dfa(time.series = fbm, npoints = 50, 
#'                    window.size.range=c(10,300), 
#'                    do.plot=FALSE)
#' fbm.estimation = estimate(dfa.analysis,do.plot = TRUE,
#'                           add.legend=F, main="DFA of fBm")
#' cat("Theorical: 1.25 ---Estimated: ",fbm.estimation ,"\n")
#' 
#' }
#' @references Penzel, Thomas, et al. "Comparison of detrended fluctuation 
#' analysis and spectral analysis for heart rate variability in sleep and 
#' sleep apnea." Biomedical Engineering, IEEE Transactions on 50.10 (2003): 
#' 1143-1151.
#' @rdname dfa
#' @export dfa
#' @import Rcpp
#' @exportClass dfa
dfa = function(time.series, window.size.range = c(10, 300),
               npoints = 20, do.plot = TRUE, ...) {
  window.sizes = c()
  fluctuation.function = c()
  
  if ((window.size.range[[2]] < window.size.range[[1]]) ||
      any(window.size.range < 1)) {
    stop("Invalid window size range")
  }
  # compute windows' sizes 
  if (npoints >= (window.size.range[[2]] - window.size.range[[1]] + 1)) {
    # compute Fn for all possible windows
    window.sizes = window.size.range[[1]]:window.size.range[[2]]
  }else{
    # Try equally spaced windows in log scale
    log.window.sizes = seq(log10(window.size.range[[1]]),
                           log10(window.size.range[[2]]),
                           len = npoints)
    window.sizes = unique(round(10 ^ log.window.sizes))
    # if there are repeated elements we select missing windows until
    # reaching npoints
    if (length(window.sizes) < npoints) { 
      missing = setdiff(window.size.range[[1]]:window.size.range[[2]],
                        window.sizes)
      points.needed = npoints - length(window.sizes) 
      add.points = missing[seq(1, points.needed, len = points.needed)]
      window.sizes = sort(c(window.sizes, add.points))
    }
  }
  npoints = length(window.sizes)
  # integrate the time series time.series: this is called the "profile" in 
  # Penzel et al.
  Y = cumsum(time.series - mean(time.series))
  
  # Calculate the local trend for
  # each of the segments by a least-square fit
  # of the time.series and compute the error
  fluctuation.function = (
    .Call('_nonlinearTseries_calculate_fluctuation_function',
          PACKAGE = 'nonlinearTseries', Y, window.sizes)
  )
  
  #create dfa object
  dfa.structure = list(window.sizes = window.sizes, 
                       fluctuation.function = fluctuation.function)
  class(dfa.structure) = "dfa"
  # add attributes
  id = deparse(substitute(time.series))
  attr(dfa.structure,"id") = id
  
  #plot
  if (do.plot) {
    tryCatch(plot(dfa.structure, ...), error = function(error){
      warning("Error while trying to plot the DFA")
    })
  }
  dfa.structure
}

#' Returns the window sizes used for DFA in a \emph{dfa} object.
#' @param x A \emph{dfa} object.
#' @return The \emph{windowSizes} function returns the windows sizes used
#' to detrend the time series in the DFA. 
#' @seealso \code{\link{dfa}}
#' @export windowSizes
windowSizes = function(x){
  UseMethod("windowSizes")
}

#' @return The \emph{windowSizes} function returns the windows sizes used
#' to detrend the time series. 
#' @rdname dfa
#' @export
windowSizes.dfa = function(x){
  x$window.sizes
}

#' Returns the fluctuation function obtained in a DFA and represented by a
#' \emph{dfa} object.
#' @param x A \emph{dfa} object.
#' @return The \emph{fluctuationFunction} function returns the fluctuation 
#' function used obtained in the DFA. 
#' @seealso \code{\link{dfa}}
#' @export fluctuationFunction
fluctuationFunction = function(x){
  UseMethod("fluctuationFunction")
}

#' @return The \emph{fluctuationFunction} function returns the fluctuation 
#' function obtained in the DFA represented by the \emph{dfa} object.
#' @rdname dfa
#' @export
fluctuationFunction.dfa = function(x){
  x$fluctuation.function
}

#' @rdname dfa
#' @param main A title for the plot.
#' @param xlab A title for the x axis.
#' @param ylab A title for the y axis.
#' @param log A character string which contains "x" if the x axis is to be 
#' logarithmic, "y" if the y axis is to be logarithmic and "xy" or "yx" if 
#' both axes are to be logarithmic.
#' @export
plot.dfa = function(x, main = "Detrended Fluctuation Analysis",
                    xlab = "Window size: t",
                    ylab = "Fluctuation function: F(t)",
                    log = "xy", ...){
  plot(x$window.sizes, x$fluctuation.function,
       main = main, xlab = xlab, ylab = ylab, log = log, ...)
}

#' @rdname dfa
#' @param x A \emph{dfa} object.
#' @param regression.range Vector with 2 components denoting the range where 
#' the function will perform linear regression.
#' @param fit.col A colors to plot the regression line.
#' @param fit.lty The type of line to plot the regression line.
#' @param fit.lwd The width of the line for the regression line.
#' @param add.legend add a legend with the resulting estmation to the plot?
#' @export
estimate.dfa = function(x, regression.range = NULL, do.plot = FALSE, 
                        fit.col=2, fit.lty = 1, fit.lwd = 1, 
                        add.legend = TRUE, ...) {
  log.fluctuation.function = log10(x$fluctuation.function)
  log.window.sizes = log10(x$window.sizes)
  if (is.null(regression.range)) {
    regression.range = range(x$window.sizes)
  }
  # prepare interpolations to calculate the exponents
  index.alpha = which(x$window.sizes >= regression.range[[1]] &
                        x$window.sizes <= regression.range[[2]])
  # get alpha
  interp1 = lm(log.fluctuation.function[index.alpha] ~ log.window.sizes[index.alpha])
  alpha = interp1$coefficients[[2]]
  if (do.plot) {
    plot(x,...)
    lines(x$window.sizes[index.alpha],10^interp1$fitted.values,
          col = fit.col, lty = fit.lty, lwd = fit.lwd)
    if (add.legend) {
      legend("bottomright", col = fit.col, lty = fit.lty, lwd = fit.lwd,
             bty = "n", legend = paste("Scaling exponent estimate =", 
                                       sprintf("%.2f", alpha))
      )
    }
  }
  attr(alpha, "fitted") = list(x = x$window.sizes[index.alpha],
                               y = 10 ^ interp1$fitted.values)
  alpha
}

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nonlinearTseries documentation built on May 2, 2019, 5:47 p.m.