R/plot_f.R

In primer: Functions and Data for the Book, a Primer of Ecology with R

#' plot_f
#'
#' Function to plot a time series and its periodogram, and calculate the
#' confidence interval of 2 times the spectral power.
#'
#'
#' @param z numeric vector.
#' @author Hank Stevens
#' @seealso [one_over_f()] to generate 1/f noise; [spec_mimic()] to rearrange
#' one vector, X, to mimic the spectrum of another vector; [spectrum()] for the
#' hard work.
#' @references J. M. Halley. Ecology, evolution and 1/f-noise. Trends in
#' Ecology & Evolution, 11:33-37, 1996. O. L. Petchey, A. Gonzalez, and H. B.
#' Wilson. Effects on population persistence: the interaction between
#' environmental noise colour, intra-specific competition and space.
#' Proceedings of the Royal Society of London Series B, 264:1841-1847, 1997. J.
#' E. Cohen, C. M. Newman, A. E. Cohen, O. L. Petchey, and A. Gonzalez.
#' Spectral mimicry: a method of synthesizing matching time series with
#' different Fourier spectra. Circuits, Systems and Signal Processing,
#' 18:431-442, 1999.
#' @keywords 1/f color-mimicry noise periodogram spectra
#' @examples
#'
#'
#' ## white noise
#' plot_f(z=runif(50))
#'
#' plot_f
#'
#' @export plot_f
plot_f <- function(z){
## plotting function, which also estimates of the slope of
## log(amplitude) - log(freq)
##
n <- length(z)
z1 <- z[1:(n/2)][-1]
spz <- stats::spectrum(z1)
lsa <- log(spz$spec)
lf <- log(spz$freq)
m <- stats::lm(lsa~lf)
graphics::par(mfrow=c(1,2))
plot(1:n, z, type='l')
plot(lf, lsa)
graphics::abline(m)
stats::confint(m)[2,]
}