R: Class '"RLum.Analysis"'

RLum.Analysis-class {Luminescence}

R Documentation

Class `"RLum.Analysis"`

Description

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 signature 'RLum.Analysis'
show(object)

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

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

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

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

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

Arguments

`object`	`get_RLum`: `names_RLum`, `length_RLum`, `structure_RLum` (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` (the default) and the result of the `get_RLum()` request is a single object this object will be unlisted, means only the object itself and no list containing exactly one object is returned. Mostly this makes things easier, however, if this method is used within a loop this might be undesired.
`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): extents 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.
`...`	further arguments passed to underlying methods

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

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 objects (same as shown with the show method)
smooth_RLum(RLum.Analysis): Smoothing of RLum.Data objects contained in this RLum.Analysis object zoo::rollmean or zoo::rollmedian. In particular the internal function .smoothing is used.

Slots

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

Objects from the Class

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

Class version

0.4.16

How to cite

Kreutzer, S., 2024. 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., 2024. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.24. https://CRAN.R-project.org/package=Luminescence

Note

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

Author(s)

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

Examples


showClass("RLum.Analysis")

##set empty object
set_RLum(class = "RLum.Analysis")

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

##show curves in object
get_RLum(IRSAR.RF.Data)

##show only the first object, but by keeping the object
get_RLum(IRSAR.RF.Data, record.id = 1, drop = FALSE)

[Package Luminescence version 0.9.24 Index]

Class "RLum.Analysis"