# apply_CosmicRayRemoval

##### Function to remove cosmic rays from an RLum.Data.Spectrum S4 class object

The function provides several methods for cosmic ray removal and spectrum smoothing for an RLum.Data.Spectrum S4 class object

- Keywords
- manip

##### Usage

```
apply_CosmicRayRemoval(object, method = "smooth",
method.Pych.smoothing = 2, method.Pych.threshold_factor = 3,
MARGIN = 2, verbose = FALSE, plot = FALSE, ...)
```

##### Arguments

- object
'>RLum.Data.Spectrum (

**required**): S4 object of class`RLum.Data.Spectrum`

- method
character (

*with default*): Defines method that is applied for cosmic ray removal. Allowed methods are`smooth`

, the default, (smooth),`smooth.spline`

(smooth.spline) and`Pych`

. See details for further information.- method.Pych.smoothing
integer (

*with default*): Smoothing parameter for cosmic ray removal according to Pych (2003). The value defines how many neighboring values in each frame are used for smoothing (e.g.,`2`

means that the two previous and two following values are used).- method.Pych.threshold_factor
numeric (

*with default*): Threshold for zero-bins in the histogram. Small values mean that more peaks are removed, but signal might be also affected by this removal.- MARGIN
integer (

*with default*): on which part the function cosmic ray removal should be applied on:1 = along the time axis (line by line),

2 = along the wavelength axis (column by column).

**Note:**This argument currently only affects the methods`smooth`

and`smooth.spline`

- verbose
logical (

*with default*): Option to suppress terminal output.,- plot
logical (

*with default*): If`TRUE`

the histograms used for the cosmic-ray removal are returned as plot including the used threshold. Note: A separat plot is returned for each frame! Currently only for`method = "Pych"`

a graphical output is provided.- ...
further arguments and graphical parameters that will be passed to the smooth function.

##### Details

`method = "Pych"`

This method applies the cosmic-ray removal algorithm described by Pych (2003). Some aspects that are different to the publication:

For interpolation between neighbouring values the median and not the mean is used.

The number of breaks to construct the histogram is set to:

`length(number.of.input.values)/2`

For further details see references below.

`method = "smooth"`

Method uses the function smooth to remove cosmic rays.

Arguments that can be passed are: `kind`

, `twiceit`

`method = "smooth.spline"`

Method uses the function smooth.spline to remove cosmic rays.

Arguments that can be passed are: `spar`

**How to combine methods?**

Different methods can be combined by applying the method repeatedly to the dataset (see example).

##### Value

##### Function version

0.2.1 (2018-01-21 17:22:38)

##### How to cite

Kreutzer, S. (2018). apply_CosmicRayRemoval(): Function to remove cosmic rays from an RLum.Data.Spectrum S4 class object. Function version 0.2.1. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J. (2018). Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.8.6. https://CRAN.R-project.org/package=Luminescence

##### References

Pych, W., 2003. A Fast Algorithm for Cosmic-Ray Removal from Single Images. Astrophysics 116, 148-153. http://arxiv.org/pdf/astro-ph/0311290.pdf?origin=publication_detail

##### See Also

'>RLum.Data.Spectrum, smooth, smooth.spline, apply_CosmicRayRemoval

##### Examples

```
# NOT RUN {
##(1) - use with your own data and combine (uncomment for usage)
## run two times the default method and smooth with another method
## your.spectrum <- apply_CosmicRayRemoval(your.spectrum, method = "Pych")
## your.spectrum <- apply_CosmicRayRemoval(your.spectrum, method = "Pych")
## your.spectrum <- apply_CosmicRayRemoval(your.spectrum, method = "smooth")
# }
```

*Documentation reproduced from package Luminescence, version 0.8.6, License: GPL-3*