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

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

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.

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

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

`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).

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

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

# 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") # }