fit_peaks: Refine position and value of extremes by fitting

In photobiology: Photobiological Calculations

Refine position and value of extremes by fitting

Description

Functions implementing fitting of peaks in a class-agnostic way. The fitting refines the location of peaks and value of peaks based on the location of maxima and minima supplied. This function is to be used together with find_peaks() or find_valleys().

Usage

fit_peaks(
  x,
  peaks.idx,
  span,
  x.col.name = NULL,
  y.col.name,
  method,
  max.span = 5L,
  maximum = TRUE,
  keep.cols = NULL
)

fit_valleys(
  x,
  valleys.idx,
  span,
  x.col.name = NULL,
  y.col.name,
  method,
  max.span = 5L,
  maximum = FALSE,
  keep.cols = NULL
)

Arguments

x	generic_spct or data.frame object.
peaks.idx, valleys.idx	logical or integer Indexes into x selecting global or local extremes.
span	odd integer The span used when refining the location of maxima or minima of x.
x.col.name, y.col.name	character Name of the column of x on which to operate.
method	character The method to use for the fit.
max.span	odd integer The maximum number of data points used when when refining the location of maxima and minima.
maximum	logical A flag indicating whether to search for maxima or minima.
keep.cols	logical Keep unrecognized columns in data frames

Details

The only method currently implemented is "spline" based on a call to splinefun in a window of width span centred on each peak pointed at by peaks.idx. A spline fitted to a narrow window will usually locate the position of the peak in the column named by the argument passed to x.col.name better than estimating the true height of the peak in the column named by the argument passed to y.col.name.

Value

An R object of the same class as x containing the fitted values for the peaks, and optionally the unmodified values at the rows matching peaks.idx or valleys.idx for other retained columns.

Note

These functions are not meant for everyday use. Use option refine.wl = TRUE of methods peaks() and valleys() instead.

Examples

peaks <- find_peaks(sun.spct[["s.e.irrad"]], span = 31)
fit_peaks(sun.spct, peaks, span = 31,
          y.col.name = "s.e.irrad", method = "spline")

photobiology documentation built on June 8, 2025, 10:14 a.m.