Class

Object class to represent analysis data for protocol analysis, i.e. all curves, spectra etc. from one measurements. Objects from this class are produced, by e.g. read_XSYG2R, read_Daybreak2R

Usage

# S4 method for class 'RLum.Analysis'
show(object)

# S4 method for class 'RLum.Analysis'
set_RLum(
  class,
  originator,
  .uid,
  .pid,
  protocol = NA_character_,
  records = list(),
  info = list()
)

# S4 method for class 'RLum.Analysis'
get_RLum(
  object,
  record.id = NULL,
  recordType = NULL,
  curveType = NULL,
  RLum.type = NULL,
  protocol = "UNKNOWN",
  get.index = NULL,
  drop = TRUE,
  recursive = TRUE,
  info.object = NULL,
  subset = NULL,
  env = parent.frame(2)
)

# S4 method for class 'RLum.Analysis'
structure_RLum(object, fullExtent = FALSE)

# S4 method for class 'RLum.Analysis'
length_RLum(object)

# S4 method for class 'RLum.Analysis'
names_RLum(object)

# S4 method for class 'RLum.Analysis'
add_metadata(object, info_element) <- value

# S4 method for class 'RLum.Analysis'
rename_metadata(object, info_element) <- value

# S4 method for class 'RLum.Analysis'
replace_metadata(object, info_element, subset = NULL) <- value

# S4 method for class 'RLum.Analysis'
smooth_RLum(object, ...)

# S4 method for class 'RLum.Analysis'
sort_RLum(object, slot = NULL, info_element = NULL, decreasing = FALSE, ...)

# S4 method for class 'RLum.Analysis'
melt_RLum(object)

# S4 method for class 'RLum.Analysis'
view(object, ...)

Arguments

object

(required): an object of class RLum.Analysis

class

set_RLum character (required): name of the RLum class to be created

originator

set_RLum character (automatic): contains the name of the calling function (the function that produces this object); can be set manually.

.uid

set_RLum character (automatic): sets an unique ID for this object using the internal C++ function create_UID.

.pid

set_RLum character (with default): option to provide a parent id for nesting at will.

protocol

set_RLum character (optional): sets protocol type for analysis object. Value may be used by subsequent analysis functions.

records

set_RLum list (required): list of RLum.Analysis objects

info

set_RLum list (optional): a list containing additional info data for the object

set_RLum:

Returns an RLum.Analysis object.

record.id

get_RLum: numeric or logical (optional): IDs of specific records. If of type logical the entire id range is assumed and TRUE and FALSE indicates the selection.

recordType

get_RLum: character (optional): record type (e.g., "OSL"). Can be also a vector, for multiple matching, e.g., recordType = c("OSL", "IRSL")

curveType

get_RLum: character (optional): curve type (e.g. "predefined" or "measured")

RLum.type

get_RLum: character (optional): RLum object type. Defaults to "RLum.Data.Curve" and "RLum.Data.Spectrum".

get.index

get_RLum: logical (optional): return a numeric vector with the index of each element in the RLum.Analysis object.

drop

get_RLum: logical (with default): coerce to the next possible layer (which are RLum.Data-objects), drop = FALSE keeps the original RLum.Analysis

recursive

get_RLum: logical (with default): if TRUE (default) when the result of the get_RLum() request is a single object, the object itself will be returned directly, rather than being wrapped in a list. Mostly this makes things easier, but this might be undesired if this method is used within a loop.

info.object

get_RLum: character (optional): name of the wanted info element

subset

get_RLum: expression (optional): logical expression indicating elements or rows to keep: missing values are taken as false. This argument takes precedence over all other arguments, meaning they are not considered when subsetting the object.

env

get_RLum: environment (with default): An environment passed to eval as the enclosure. This argument is only relevant when subsetting the object and should not be used manually.

fullExtent

structure_RLum; logical (with default): extends the returned data.frame to its full extent, i.e. all info elements are part of the return as well. The default value is FALSE as the data frame might become rather big.

info_element

character (optional): name of the info field to use in sorting.

value

(required) The value assigned to the selected elements of the metadata field. If NULL the elements named in info_element will be removed.

...

other arguments that might be passed

slot

character (optional): slot name to use in sorting.

decreasing

logical (with default): whether the sort order should be decreasing (FALSE by default).

Value

get_RLum:

Returns:

list of RLum.Data objects or
Single RLum.Data object, if only one object is contained and recursive = FALSE or
RLum.Analysis objects for drop = FALSE

structure_RLum:

Returns data.frame showing the structure.

length_RLum

Returns the number records in this object.

names_RLum

Returns the names of the record types (recordType) in this object.

smooth_RLum

Same object as input, after smoothing

sort_RLum

Same object as input, but sorted according to the specified parameters.

melt_RLum

Flat data.frame with X, Y, TYPE, UID

Methods (by generic)

show(RLum.Analysis): Show structure of RLum.Analysis object
set_RLum(RLum.Analysis): Construction method for RLum.Analysis objects.
get_RLum(RLum.Analysis): Accessor method for RLum.Analysis object.

The slots record.id, @recordType, @curveType and @RLum.type are optional to allow for records limited by their id (list index number), their record type (e.g. recordType = "OSL") or object type.

Example: curve type (e.g. curveType = "predefined" or curveType ="measured")

The selection of a specific RLum.type object superimposes the default selection. Currently supported objects are: RLum.Data.Curve and RLum.Data.Spectrum
structure_RLum(RLum.Analysis): Method to show the structure of an RLum.Analysis object.
length_RLum(RLum.Analysis): Returns the length of the object, i.e., number of stored records.
names_RLum(RLum.Analysis): Returns the names of the RLum.Data objects (same as shown with the show method)
add_metadata(RLum.Analysis) <- value: Adds metadata to RLum.Analysis objects
rename_metadata(RLum.Analysis) <- value: Renames a metadata entry of RLum.Analysis objects
replace_metadata(RLum.Analysis) <- value: Replaces or removes metadata of RLum.Analysis objects
smooth_RLum(RLum.Analysis): Smoothing of RLum.Data objects contained in this RLum.Analysis object using the internal function .smoothing.
sort_RLum(RLum.Analysis): Sorting of RLum.Data objects contained in this RLum.Analysis object. At least one of slot and info_element must be provided. If both are given, ordering by slot always supersedes ordering by info_element.
melt_RLum(RLum.Analysis): Melts RLum.Analysis objects into a flat data.frame to be used in combination with other packages such as ggplot2.
view(RLum.Analysis): View method for RLum.Analysis objects

Slots

protocol: Object of class character describing the applied measurement protocol
records: Object of class list containing objects of class RLum.Data

Note

The method structure_RLum is currently just available for objects containing RLum.Data.Curve.

Objects from the Class

Objects can be created by calls of the form set_RLum("RLum.Analysis", ...).

Class version

0.4.18

Author

Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany) , RLum Developer Team

How to cite

Kreutzer, S., 2025. RLum.Analysis-class(): Class 'RLum.Analysis'. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., Mercier, N., Philippe, A., Riedesel, S., Autzen, M., Mittelstrass, D., Gray, H.J., Galharret, J., Colombo, M., Steinbuch, L., Boer, A.d., 2025. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 1.0.1. https://r-lum.github.io/Luminescence/

Examples


showClass("RLum.Analysis")
#> Class "RLum.Analysis" [package "Luminescence"]
#> 
#> Slots:
#>                                                                         
#> Name:    protocol    records originator       info       .uid       .pid
#> Class:  character       list  character       list  character  character
#> 
#> Extends: "RLum"

##set empty object
set_RLum(class = "RLum.Analysis")
#> 
#>  [RLum.Analysis-class]
#> 	 originator: eval()
#> 	 protocol: NA
#> 	 additional info elements:  0
#> 	 number of records: 0
#> 	 >> This is an empty object, which cannot be used for further analysis! <<

###use example data
##load data
data(ExampleData.RLum.Analysis, envir = environment())

##show curves in object
get_RLum(IRSAR.RF.Data)
#> [[1]]
#> 
#>  [RLum.Data.Curve-class]
#> 	 recordType: RF
#> 	 curveType: NA
#> 	 measured values: 5
#> 	 .. range of x-values: 0.1747448 6.311132
#> 	 .. range of y-values: 1423.15 1437.8 
#> 	 additional info elements: 0 
#> 
#> [[2]]
#> 
#>  [RLum.Data.Curve-class]
#> 	 recordType: RF
#> 	 curveType: NA
#> 	 measured values: 524
#> 	 .. range of x-values: 0.3768403 715.4821
#> 	 .. range of y-values: 1379.947 2103.4 
#> 	 additional info elements: 0 
#> 

##show only the first object, but by keeping the object
get_RLum(IRSAR.RF.Data, record.id = 1, drop = FALSE)
#> 
#>  [RLum.Analysis-class]
#> 	 originator: NA()
#> 	 protocol: IRSAR
#> 	 additional info elements:  0
#> 	 number of records: 1
#> 	 .. : RLum.Data.Curve : 1
#> 	 .. .. : #1 RF

Class `"RLum.Analysis"`