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Peaks or local maxima

Source: R/spct.peaks.r
peaks.Rd

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,
  x.var.name = NULL,
  y.var.name = NULL,
  var.name = y.var.name,
  refine.wl = FALSE,
  method = "spline",
  ...
)

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

# 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"),
  refine.wl = FALSE,
  method = "spline",
  ...
)

# 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"),
  refine.wl = FALSE,
  method = "spline",
  ...
)

# 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"),
  refine.wl = FALSE,
  method = "spline",
  ...
)

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

# S3 method for class 'solute_spct'
peaks(
  x,
  span = 5,
  ignore_threshold = 0,
  strict = TRUE,
  na.rm = FALSE,
  refine.wl = FALSE,
  method = "spline",
  ...
)

# S3 method for class 'cps_spct'
peaks(
  x,
  span = 5,
  ignore_threshold = 0,
  strict = TRUE,
  na.rm = FALSE,
  var.name = "cps",
  refine.wl = FALSE,
  method = "spline",
  ...
)

# S3 method for class 'raw_spct'
peaks(
  x,
  span = 5,
  ignore_threshold = 0,
  strict = TRUE,
  na.rm = FALSE,
  var.name = "counts",
  refine.wl = FALSE,
  method = "spline",
  ...
)

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

# S3 method for class 'source_mspct'
peaks(
  x,
  span = 5,
  ignore_threshold = 0,
  strict = TRUE,
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  refine.wl = FALSE,
  method = "spline",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'response_mspct'
peaks(
  x,
  span = 5,
  ignore_threshold = 0,
  strict = TRUE,
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  refine.wl = FALSE,
  method = "spline",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'filter_mspct'
peaks(
  x,
  span = 5,
  ignore_threshold = 0,
  strict = TRUE,
  na.rm = FALSE,
  filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
  refine.wl = FALSE,
  method = "spline",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

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

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

# S3 method for class 'cps_mspct'
peaks(
  x,
  span = 5,
  ignore_threshold = 0,
  strict = TRUE,
  na.rm = FALSE,
  var.name = "cps",
  refine.wl = FALSE,
  method = "spline",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'raw_mspct'
peaks(
  x,
  span = 5,
  ignore_threshold = 0,
  strict = TRUE,
  na.rm = FALSE,
  var.name = "counts",
  refine.wl = FALSE,
  method = "spline",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

x

an R object

span

integer 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. Use NULL for the global peak.

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. Negative values set a threshold so that the tallest peaks are ignored, instead of the shortest.

strict

logical If TRUE, an element must be strictly greater than all other values in its window to be considered a peak.

na.rm

logical indicating whether NA values should be stripped before searching for peaks.

...

ignored

var.name, x.var.name, y.var.name

character Name of column where to look for peaks.

refine.wl

logical Flag indicating if peak location should be refined by fitting a function.

method

character String with the name of a method. Currently only spline interpolation is implemented.

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)

  • peaks(default): Default returning always NA.

  • peaks(numeric): Default function usable on numeric vectors.

  • peaks(data.frame): Method for "data.frame" objects.

  • peaks(generic_spct): Method for "generic_spct" objects.

  • peaks(source_spct): Method for "source_spct" objects.

  • peaks(response_spct): Method for "response_spct" objects.

  • peaks(filter_spct): Method for "filter_spct" objects.

  • peaks(reflector_spct): Method for "reflector_spct" objects.

  • peaks(solute_spct): Method for "solute_spct" objects.

  • peaks(cps_spct): Method for "cps_spct" objects.

  • peaks(raw_spct): Method for "raw_spct" objects.

  • peaks(generic_mspct): Method for "generic_mspct" objects.

  • peaks(source_mspct): Method for "source_mspct" objects.

  • peaks(response_mspct): Method for "cps_mspct" objects.

  • peaks(filter_mspct): Method for "filter_mspct" objects.

  • peaks(reflector_mspct): Method for "reflector_mspct" objects.

  • peaks(solute_mspct): Method for "solute_mspct" objects.

  • peaks(cps_mspct): Method for "cps_mspct" objects.

  • peaks(raw_mspct): Method for "raw_mspct" objects.

Note

Thresholds for ignoring peaks are applied after peaks are searched for, and negative threshold values can in some cases result in no peaks being returned.

See also

Other peaks and valleys functions: find_peaks(), find_spikes(), get_peaks(), replace_bad_pixs(), spikes(), valleys(), wls_at_target()

Examples

peaks(sun.spct, span = 51)
#> Object: source_spct [3 x 2]
#> Wavelength range 451-747 nm, step 44-252 nm 
#> Label: sunlight, simulated 
#> Measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI 
#> Variables:
#>  w.length: Wavelength [nm]
#>  s.e.irrad: Spectral energy irradiance [W m-2 nm-1] 
#> --
#> # A tibble: 3 × 2
#>   w.length s.e.irrad
#>      <dbl>     <dbl>
#> 1      451     0.820
#> 2      495     0.790
#> 3      747     0.503
peaks(sun.spct, span = NULL)
#> Object: source_spct [1 x 2]
#> Wavelength range 451-451 nm, step NA nm 
#> Label: sunlight, simulated 
#> Measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI 
#> Variables:
#>  w.length: Wavelength [nm]
#>  s.e.irrad: Spectral energy irradiance [W m-2 nm-1] 
#> --
#> # A tibble: 1 × 2
#>   w.length s.e.irrad
#>      <dbl>     <dbl>
#> 1      451     0.820
peaks(sun.spct, span = 51, refine.wl = TRUE)
#> Object: source_spct [3 x 2]
#> Wavelength range 451.02686-747.52003 nm, step 44.07624-252.4169 nm 
#> Label: sunlight, simulated 
#> Measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI 
#> Variables:
#>  w.length: Wavelength [nm]
#>  s.e.irrad: Spectral energy irradiance [W m-2 nm-1] 
#> --
#> # A tibble: 3 × 2
#>   w.length s.e.irrad
#>      <dbl>     <dbl>
#> 1     451.     0.821
#> 2     495.     0.791
#> 3     748.     0.503

peaks(sun.spct)
#> Object: source_spct [76 x 2]
#> Wavelength range 321-798 nm, step 3-20 nm 
#> Label: sunlight, simulated 
#> Measured on 2010-06-22 09:51:00 UTC 
#> Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI 
#> Variables:
#>  w.length: Wavelength [nm]
#>  s.e.irrad: Spectral energy irradiance [W m-2 nm-1] 
#> --
#> # A tibble: 76 × 2
#>    w.length s.e.irrad
#>       <dbl>     <dbl>
#>  1      321     0.182
#>  2      330     0.330
#>  3      335     0.313
#>  4      340     0.335
#>  5      343     0.338
#>  6      347     0.321
#>  7      350     0.345
#>  8      354     0.376
#>  9      360     0.371
#> 10      366     0.449
#> # ℹ 66 more rows