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Spikes

Source: R/spct.spikes.R
spikes.Rd

Function that returns a subset of an R object with observations corresponding to spikes. Spikes are values in spectra that are unusually high compared to neighbors. They are usually individual values or very short runs of similar "unusual" values. Spikes caused by cosmic radiation are a frequent problem in Raman spectra. Another source of spikes are "hot pixels" in CCD and diode arrays.

Usage

spikes(x, z.threshold, max.spike.width, na.rm, ...)

# Default S3 method
spikes(x, z.threshold = NA, max.spike.width = 8, na.rm = FALSE, ...)

# S3 method for class 'numeric'
spikes(x, z.threshold = NA, max.spike.width = 8, na.rm = FALSE, ...)

# S3 method for class 'data.frame'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  ...,
  y.var.name = NULL,
  var.name = y.var.name
)

# S3 method for class 'generic_spct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  var.name = NULL,
  ...
)

# S3 method for class 'source_spct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)

# S3 method for class 'response_spct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)

# S3 method for class 'filter_spct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
  ...
)

# S3 method for class 'reflector_spct'
spikes(x, z.threshold = 9, max.spike.width = 8, na.rm = FALSE, ...)

# S3 method for class 'solute_spct'
spikes(x, z.threshold = 9, max.spike.width = 8, na.rm = FALSE, ...)

# S3 method for class 'cps_spct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  var.name = "cps",
  ...
)

# S3 method for class 'raw_spct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  var.name = "counts",
  ...
)

# S3 method for class 'generic_mspct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  ...,
  var.name = NULL,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'source_mspct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'response_mspct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'filter_mspct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'reflector_mspct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'solute_mspct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'cps_mspct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  ...,
  var.name = "cps",
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'raw_mspct'
spikes(
  x,
  z.threshold = 9,
  max.spike.width = 8,
  na.rm = FALSE,
  ...,
  var.name = "counts",
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

x

an R object

z.threshold

numeric Modified Z values larger than z.threshold are considered to correspond to spikes.

max.spike.width

integer Wider regions with high Z values are not detected as spikes.

na.rm

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

...

ignored

var.name, y.var.name

character Name of column where to look for spikes.

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 the object passed as argument to x with rows corresponding to spikes.

Details

Spikes are detected based on a modified Z score calculated from the differenced spectrum. The Z threshold used should be adjusted to the characteristics of the input and desired sensitivity. The lower the threshold the more stringent the test becomes, resulting in most cases in more spikes being detected. A modified version of the algorithm is used if a value different from NULL is passed as argument to max.spike.width. In such a case, an additional step filters out broader spikes (or falsely detected steep slopes) from the returned values.

When the argument passed to x contains multiple spectra, the spikes are searched for in each spectrum independently of other spectra.

Methods (by class)

  • spikes(default): Default returning always NA.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See also

See the documentation for find_spikes for details of the algorithm and implementation.

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

Examples

spikes(sun.spct)
#> Object: source_spct [2 x 2]
#> Wavelength range 398-432 nm, step 34 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: 2 × 2
#>   w.length s.e.irrad
#>      <dbl>     <dbl>
#> 1      398     0.504
#> 2      432     0.646