spikes: Spikes
In photobiology: Photobiological Calculations

spikes

R Documentation

Spikes

Description

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.