Finds local maxima in sequential data.
peaks_find(x, y, ...) # S4 method for numeric,numeric peaks_find(x, y, method = "MAD", SNR = 2, m = NULL, ...) # S4 method for ANY,missing peaks_find(x, method = "MAD", SNR = 2, m = NULL, ...)
- x, y
Extra parameters to be passed to internal methods.
characterstring specifying the method to be used for background noise estimation (see below).
integergiving the signal-to-noise-ratio for peak detection (see below).
integergiving the window size (i.e. the number of adjacent points to be used). If
NULL, 5% of the data points is used as the half window size.
list with two components
A local maximum has to be the highest one in the given window and has to be higher than \(SNR \times noise\) to be recognized as peak.
The following methods are available for noise estimation:
Median Absolute Deviation.
Note that to improve peak detection, it may be helpful to smooth the data and remove the baseline beforehand.
There will be \((m - 1) / 2\) points both at the beginning and at the end of the data series for which a complete \(m\)-width window cannot be obtained. To prevent data loss, progressively wider/narrower windows are used at both ends of the data series.
Adapted from Stasia Grinberg's
Other peaks detection methods:
## X-ray diffraction data("XRD") ## Whittaker smoothing smooth <- smooth_whittaker(XRD, lambda = 1000, d = 2, sparse = TRUE) ## 4S Peak Filling baseline baseline <- baseline_peakfilling(smooth, n = 10, m = 5, by = 10) plot(XRD, type = "l", xlab = expression(2*theta), ylab = "Count") lines(baseline, type = "l", col = "red") ## Correct baseline XRD <- signal_drift(XRD, lag = baseline, subtract = TRUE) ## Find peaks peaks <- peaks_find(XRD, SNR = 3, m = 11) plot(XRD, type = "l", xlab = expression(2*theta), ylab = "Count") lines(peaks, type = "p", pch = 16, col = "red") abline(h = attr(peaks, "noise"), lty = 2) # noise threshold ## Half-Width at Half-Maximum x <- seq(-4, 4, length = 1000) y <- dnorm(x) peaks_fwhm(x, y, center = 0) # Expected: 2 * sqrt(2 * log(2)) #>  2.354354