R: Peaks or local maxima

peaks {photobiology} | R Documentation

## Peaks or local maxima

### Description

Function that returns a subset of an R object with observations corresponding to local maxima.

### Usage

    peaks(x, span, ignore_threshold, strict, na.rm, ...)

    ## Default S3 method:
    peaks(x, span = NA, ignore_threshold = NA, strict = NA,
      na.rm = FALSE, ...)

    ## S3 method for class 'numeric'
    peaks(x, span = 5, ignore_threshold = NA, strict = TRUE,
      na.rm = FALSE, ...)

    ## S3 method for class 'data.frame'
    peaks(x, span = 5, ignore_threshold = 0,
      strict = TRUE, na.rm = FALSE, var.name, ...)

    ## S3 method for class 'generic_spct'
    peaks(x, span = 5, ignore_threshold = 0,
      strict = TRUE, na.rm = FALSE, var.name = NULL, ...)

    ## S3 method for class 'source_spct'
    peaks(x, span = 5, ignore_threshold = 0,
      strict = TRUE, na.rm = FALSE,
      unit.out = getOption("photobiology.radiation.unit", default = "energy"),
      ...)

    ## S3 method for class 'response_spct'
    peaks(x, span = 5, ignore_threshold = 0,
      strict = TRUE, na.rm = FALSE,
      unit.out = getOption("photobiology.radiation.unit", default = "energy"),
      ...)

    ## S3 method for class 'filter_spct'
    peaks(x, span = 5, ignore_threshold = 0,
      strict = TRUE, na.rm = FALSE,
      filter.qty = getOption("photobiology.filter.qty", default =
      "transmittance"), ...)

    ## S3 method for class 'reflector_spct'
    peaks(x, span = 5, ignore_threshold = 0,
      strict = TRUE, na.rm = FALSE, ...)

    ## S3 method for class 'cps_spct'
    peaks(x, span = 5, ignore_threshold = 0, strict = TRUE,
      na.rm = FALSE, ...)

    ## S3 method for class 'generic_mspct'
    peaks(x, span = 5, ignore_threshold = 0,
      strict = TRUE, na.rm = FALSE, ..., .parallel = FALSE, .paropts = NULL)

### Arguments

`x` | an R object
`span` | a peak is defined as an element in a sequence which is greater than all other elements within a window of width span centered at that element. The default value is 3, meaning that a peak is bigger than both of its neighbors. Default: 3.
`ignore_threshold` | numeric value between 0.0 and 1.0 indicating the relative size compared to tallest peak threshold below which peaks will be ignored.
`strict` | logical flag: if TRUE, an element must be strictly greater than all other values in its window to be considered a peak. Default: TRUE.
`na.rm` | logical indicating whether `NA` values should be stripped before searching for peaks.
`...` | ignored
`var.name` | Name of column where to look for peaks.
`unit.out` | character One of "energy" or "photon"
`filter.qty` | character One of "transmittance" or "absorbance"
`.parallel` | if TRUE, apply function in parallel, using parallel backend provided by foreach
`.paropts` | a list of additional options passed into the foreach function when parallel computation is enabled. This is important if (for example) your code relies on external data or packages: use the .export and .packages arguments to supply them so that all cluster nodes have the correct environment set up for computing.

### Value

A subset of `x` with rows corresponding to local maxima.

### Methods (by class)

- `default`: Default returning always NA.

- `numeric`: Default function usable on numeric vectors.

- `data.frame`: Method for "data.frame" objects.

- `generic_spct`: Method for "generic_spct" objects.

- `source_spct`: Method for "source_spct" objects.

- `response_spct`: Method for "response_spct" objects.

- `filter_spct`: Method for "filter_spct" objects.

- `reflector_spct`: Method for "reflector_spct" objects.

- `cps_spct`: Method for "cps_spct" objects.

- `generic_mspct`: Method for "cps_spct" objects.

### See Also

Other peaks and valleys functions: `find_peaks`, `get_peaks`, `valleys`

### Examples

    peaks(sun.spct, span = 50)
    peaks(sun.spct, span = NULL)

    peaks(sun.spct)

[Package photobiology version 0.9.21 Index]