R: Shift the scale of a spectrum using a summary function

fshift {photobiology} | R Documentation

## Shift the scale of a spectrum using a summary function

### Description

These functions return a spectral object of the same class as the one supplied as argument but with the spectral data on a shifted scale. A range of wavelengths is taken a reference (zero or another numeric constant) and a summary is calculated for this waveband. The difference between the computed and reference value are used to shift the scale so that these two values match in the returned object.

### Usage

    fshift(x, ...)

    ## S3 method for class 'source_spct'
    fshift(x, range = c(min(x), min(x) + 10), f = "mean",
      unit.out = getOption("photobiology.radiation.unit", default = "energy"),
      ...)

    ## S3 method for class 'response_spct'
    fshift(x, range = c(min(x), min(x) + 10),
      f = "mean", unit.out = getOption("photobiology.radiation.unit", default =
      "energy"), ...)

    ## S3 method for class 'filter_spct'
    fshift(x, range = c(min(x), min(x) + 10), f = "min",
      qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
      ...)

    ## S3 method for class 'reflector_spct'
    fshift(x, range = c(min(x), min(x) + 10),
      f = "min", qty.out = NULL, ...)

    ## S3 method for class 'source_mspct'
    fshift(x, range = c(min(x), min(x) + 10), f = "mean",
      unit.out = getOption("photobiology.radiation.unit", default = "energy"),
      ...)

    ## S3 method for class 'raw_spct'
    fshift(x, range = c(min(x), min(x) + 10), f = "mean",
      qty.out = NULL, ...)

    ## S3 method for class 'cps_spct'
    fshift(x, range = c(min(x), min(x) + 10), f = "mean",
      qty.out = NULL, ...)

    ## S3 method for class 'generic_spct'
    fshift(x, range = c(min(x), min(x) + 10), f = "mean",
      col.names, ...)

    ## S3 method for class 'response_mspct'
    fshift(x, range = c(min(x), min(x) + 10),
      f = "mean", unit.out = getOption("photobiology.radiation.unit", default =
      "energy"), ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'filter_mspct'
    fshift(x, range = c(min(x), min(x) + 10), f = "min",
      qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
      ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'reflector_mspct'
    fshift(x, range = c(min(x), min(x) + 10),
      f = "min", qty.out = NULL, ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'raw_mspct'
    fshift(x, range = c(min(x), min(x) + 10), f = "min",
      ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'cps_mspct'
    fshift(x, range = c(min(x), min(x) + 10), f = "min",
      ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'generic_mspct'
    fshift(x, range = c(min(x), min(x) + 10), f = "min",
      col.names, ..., .parallel = FALSE, .paropts = NULL)

### Arguments

`x` | An R object
`...` | additional named arguments passed down to `f`.
`range` | An R object on which `range()` returns a numeric vector of length 2 with the limits of a range of wavelengths in nm, with min and max wavelengths (nm)
`f` | character string "mean", "min" or "max" for scaling so that this summary value becomes the origin of the spectral data scale in the returned object, or the name of a function taking `x` as first argument and returning a numeric value.
`unit.out` | character Allowed values "energy", and "photon", or its alias "quantum"
`qty.out` | character Allowed values "transmittance", and "absorbance"
`col.names` | character vector containing the names of columns or variables to which to apply the scale shift.
`.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 copy of `x` with the spectral data values replaced with values zero-shifted.

### Methods (by class)

- `source_spct`:

- `response_spct`:

- `filter_spct`:

- `reflector_spct`:

- `source_mspct`:

- `raw_spct`:

- `cps_spct`:

- `generic_spct`:

- `response_mspct`:

- `filter_mspct`:

- `reflector_mspct`:

- `raw_mspct`:

- `cps_mspct`:

- `generic_mspct`:

### See Also

Other rescaling functions: `fscale`, `getNormalized`, `is_normalized`, `is_scaled`, `normalize`, `setNormalized`, `setScaled`

[Package photobiology version 0.9.21 Index]