peakwindow: Identify Peaks in Multimodal Density Curves and Time Series

In tpetzoldt/antibioticR: Analysis of Antibiotic Resistance Data

Description

This function identifies peaks in multimodal empirical density functions or in time series and helps to identify the time window of the first maximum according to a given heuristics.

Usage

peakwindow(
  x,
  y = NULL,
  xstart = 0,
  xend = max(x),
  minpeak = 0.1,
  mincut = 0.382
)

Arguments

x	x coordinate of a set of points.
y	y coordinate of a set of points. Alternatively, a single argument x can be provided.
xstart	start before the maximum value of the searched peak (this is a “weak” limit)
xend	maximum of the end of the searched peak (this is a “hard” maximum)
minpeak	minimum value of the total maximum which is regarded as peak
mincut	minimum relative height of a pit compared to the lower of the two neighbouring maxima at which these maxima are regarded as separate peaks (default value is derived from golden section)

Value

A list with the following elements:

peaks	a data frame with the characteristics (index, xleft, x, xright and y) of all identified peaks,
first.max.index	index of the maximum value of the “specified” peak,
first.max.x	x-value of the maximum of the “specified” peak,
first.indices	indices (data window) of all data belonging to the “specified” peak,
first.x	x-values (time window) of all data belonging to the “specified” peak,
first.y	corresponding y-values of all data belonging to the “specified” peak,
peakid	vector with peak-id-numbers for all data.

Examples

## generate test data with 3 peaks
set.seed(123)
x <- seq(0, 360, length = 20)
y <- abs(rnorm(20, mean = 1, sd = 0.1))
y[5:10] <- c(2, 4, 7, 3, 4, 2)
y <- c(y, 0.8 * y, 1.2 * y)
x <- seq(0, 360, along = y)
y[6] <- y[7]   # test case with 2 neighbouring equal points
## plot the test data
plot(x, y, type="b")
## identify the first peak
peaks <- peakwindow(x, y)
ind <- peaks$smd.indices
lines(x[ind], y[ind], col="red", lwd=2)

## some more options ...
peaks <- peakwindow(x, y, xstart=150, mincut = 0.455)
ind <- peaks$first.indices
lines(x[ind], y[ind], col = "blue")
points(x, y, col = peaks$peakid +1, pch = 16) # all peaks

## work with indices only
peaks <- peakwindow(y)

## test case with disturbed sinus
x<- 1:100
y <- sin(x/5) +1.5 + rnorm(x, sd = 0.2)
peaks <- peakwindow(x, y)
plot(x, y, type = "l", ylim = c(0, 3))
points(x, y, col = peaks$peakid + 2, pch = 16)

## test case: only one peak
yy <- c(1:10, 11:1)
peakwindow(yy)

## error handling test case: no turnpoints
# yy <- rep(1, length(x))
# peakwindow(x, yy)

tpetzoldt/antibioticR documentation built on Sept. 25, 2021, 1:17 p.m.