R: Clean (=replace) off-range values in a spectrum

clean {photobiology} | R Documentation

## Clean (=replace) off-range values in a spectrum

### Description

These functions implement the equivalent of replace() but for spectral objects instead of vectors.

### Usage

    clean(x, range, range.s.data, fill, ...)

    ## Default S3 method:
    clean(x, range, range.s.data, fill, ...)

    ## S3 method for class 'source_spct'
    clean(x, range = x, range.s.data = c(0, NA),
      fill = range.s.data, unit.out = getOption("photobiology.radiation.unit",
      default = "energy"), ...)

    ## S3 method for class 'filter_spct'
    clean(x, range = x, range.s.data = NULL,
      fill = range.s.data, qty.out = getOption("photobiology.filter.qty",
      default = "transmittance"), ...)

    ## S3 method for class 'reflector_spct'
    clean(x, range = x, range.s.data = c(0, 1),
      fill = range.s.data, ...)

    ## S3 method for class 'response_spct'
    clean(x, range = x, range.s.data = c(0, NA),
      fill = range.s.data, unit.out = getOption("photobiology.radiation.unit",
      default = "energy"), ...)

    ## S3 method for class 'cps_spct'
    clean(x, range = x, range.s.data = c(0, NA),
      fill = range.s.data, ...)

    ## S3 method for class 'raw_spct'
    clean(x, range = x, range.s.data = c(NA_real_, NA_real_),
      fill = range.s.data, ...)

    ## S3 method for class 'generic_spct'
    clean(x, range = x, range.s.data = c(NA_real_,
      NA_real_), fill = range.s.data, col.names, ...)

    ## S3 method for class 'source_mspct'
    clean(x, range = NULL, range.s.data = c(0, NA),
      fill = range.s.data, unit.out = getOption("photobiology.radiation.unit",
      default = "energy"), ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'filter_mspct'
    clean(x, range = NULL, range.s.data = NULL,
      fill = range.s.data, qty.out = getOption("photobiology.filter.qty",
      default = "transmittance"), ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'reflector_mspct'
    clean(x, range = NULL, range.s.data = c(0, 1),
      fill = range.s.data, ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'response_mspct'
    clean(x, range = NULL, range.s.data = c(0, NA),
      fill = range.s.data, unit.out = getOption("photobiology.radiation.unit",
      default = "energy"), ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'cps_mspct'
    clean(x, range = NULL, range.s.data = c(0, NA),
      fill = range.s.data, ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'raw_mspct'
    clean(x, range = NULL, range.s.data = c(0, NA),
      fill = range.s.data, ..., .parallel = FALSE, .paropts = NULL)

    ## S3 method for class 'generic_mspct'
    clean(x, range = x, range.s.data = c(NA_real_,
      NA_real_), fill = range.s.data, col.names, ..., .parallel = FALSE,
      .paropts = NULL)

### Arguments

`x` | an R object
`range` | numeric vector of wavelengths
`range.s.data` | numeric vector of length two giving the allowable range for the spectral data.
`fill` | numeric vector of length 1 or 2, giving the replacement values to use at each extreme of the range.
`...` | currently ignored
`unit.out` | character string with allowed values "energy", and "photon", or its alias "quantum"
`qty.out` | character string with allowed values "energy", and "photon", or its alias "quantum"
`col.names` | character The name of the variable to clean
`.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`, possibly with some of the spectral data values replaced by the value passed to `fill`.

### Methods (by class)

- `default`: Default for generic function

- `source_spct`: Replace off-range values in a source spectrum

- `filter_spct`: Replace off-range values in a filter spectrum

- `reflector_spct`: Replace off-range values in a reflector spectrum

- `response_spct`: Replace off-range values in a response spectrum

- `cps_spct`: Replace off-range values in a counts per second spectrum

- `raw_spct`: Replace off-range values in a raw counts spectrum

- `generic_spct`: Replace off-range values in a generic spectrum

- `source_mspct`:

- `filter_mspct`:

- `reflector_mspct`:

- `response_mspct`:

- `cps_mspct`:

- `raw_mspct`:

- `generic_mspct`:

[Package photobiology version 0.9.21 Index]