# analyse_pIRIRSequence

##### Analyse post-IR IRSL measurement sequences

The function performs an analysis of post-IR IRSL sequences including curve fitting on '>RLum.Analysis objects.

##### Usage

```
analyse_pIRIRSequence(object, signal.integral.min, signal.integral.max,
background.integral.min, background.integral.max, dose.points = NULL,
sequence.structure = c("TL", "IR50", "pIRIR225"), plot = TRUE,
plot.single = FALSE, ...)
```

##### Arguments

- object
'>RLum.Analysis or list of '>RLum.Analysis objects (

**required**): input object containing data for analysis. If a list is provided the functions tries to iteratre over the list.- signal.integral.min
integer (

**required**): lower bound of the signal integral. Provide this value as vector for different integration limits for the different IRSL curves.- signal.integral.max
integer (

**required**): upper bound of the signal integral. Provide this value as vector for different integration limits for the different IRSL curves.- background.integral.min
integer (

**required**): lower bound of the background integral. Provide this value as vector for different integration limits for the different IRSL curves.- background.integral.max
integer (

**required**): upper bound of the background integral. Provide this value as vector for different integration limits for the different IRSL curves.- dose.points
numeric (

*optional*): a numeric vector containing the dose points values. Using this argument overwrites dose point values in the signal curves.- sequence.structure
vector character (

*with default*): specifies the general sequence structure. Allowed values are`"TL"`

and any`"IR"`

combination (e.g.,`"IR50"`

,`"pIRIR225"`

). Additionally a parameter`"EXCLUDE"`

is allowed to exclude curves from the analysis (Note: If a preheat without PMT measurement is used, i.e. preheat as none TL, remove the TL step.)- plot
logical (

*with default*): enables or disables plot output.- plot.single
logical (

*with default*): single plot output (`TRUE/FALSE`

) to allow for plotting the results in single plot windows. Requires`plot = TRUE`

.- ...
further arguments that will be passed to the function analyse_SAR.CWOSL and plot_GrowthCurve. Furthermore, the arguments

`main`

(headers),`log`

(IRSL curves),`cex`

(control the size) and`mtext.outer`

(additional text on the plot area) can be passed to influence the plotting. If the input is list,`main`

can be passed as vector or list.

##### Details

To allow post-IR IRSL protocol (Thomsen et al., 2008) measurement analyses this function has been written as extended wrapper function for the function analyse_SAR.CWOSL, facilitating an entire sequence analysis in one run. With this, its functionality is strictly limited by the functionality of the function analyse_SAR.CWOSL.

**Defining the sequence structure **

The argument `sequence.structure`

expects a shortened pattern of your sequence structure and was
mainly introduced to ease the use of the function. For example: If your measurement data contains
the following curves: `TL`

, `IRSL`

, `IRSL`

, `TL`

, `IRSL`

, `IRSL`

, the sequence pattern in `sequence.structure`

becomes `c('TL', 'IRSL', 'IRSL')`

. The second part of your sequence for one cycle should be
similar and can be discarded. If this is not the case (e.g., additional hotbleach) such curves
have to be removed before using the function.

**If the input is a list**

If the input is a list of RLum.Analysis-objects, every argument can be provided as list to allow for different sets of parameters for every single input element. For further information see analyse_SAR.CWOSL.

##### Value

Plots (*optional*) and an '>RLum.Results object is
returned containing the following elements:

DATA.OBJECT |
TYPE |
DESCRIPTION |

`..$data` : |
`data.frame` |
Table with De values |

`..$LnLxTnTx.table` : |
`data.frame` |
with the LnLxTnTx values |

`..$rejection.criteria` : |
data.frame | rejection criteria |

`..$Formula` : |
list | Function used for fitting of the dose response curve |

The output should be accessed using the function get_RLum.

##### Note

Best graphical output can be achieved by using the function `pdf`

with the following options:

`pdf(file = "...", height = 15, width = 15)`

##### Function version

0.2.4 (2018-08-02 12:37:05)

##### How to cite

Kreutzer, S. (2018). analyse_pIRIRSequence(): Analyse post-IR IRSL measurement sequences. Function version 0.2.4. 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

Murray, A.S., Wintle, A.G., 2000. Luminescence dating of quartz using an improved single-aliquot regenerative-dose protocol. Radiation Measurements 32, 57-73. doi:10.1016/S1350-4487(99)00253-X

Thomsen, K.J., Murray, A.S., Jain, M., Boetter-Jensen, L., 2008. Laboratory fading rates of various luminescence signals from feldspar-rich sediment extracts. Radiation Measurements 43, 1474-1486. doi:10.1016/j.radmeas.2008.06.002

##### See Also

analyse_SAR.CWOSL, calc_OSLLxTxRatio, plot_GrowthCurve, '>RLum.Analysis, '>RLum.Results get_RLum

##### Examples

```
# NOT RUN {
### NOTE: For this example existing example data are used. These data are non pIRIR data.
###
##(1) Compile example data set based on existing example data (SAR quartz measurement)
##(a) Load example data
data(ExampleData.BINfileData, envir = environment())
##(b) Transform the values from the first position in a RLum.Analysis object
object <- Risoe.BINfileData2RLum.Analysis(CWOSL.SAR.Data, pos=1)
##(c) Grep curves and exclude the last two (one TL and one IRSL)
object <- get_RLum(object, record.id = c(-29,-30))
##(d) Define new sequence structure and set new RLum.Analysis object
sequence.structure <- c(1,2,2,3,4,4)
sequence.structure <- as.vector(sapply(seq(0,length(object)-1,by = 4),
function(x){sequence.structure + x}))
object <- sapply(1:length(sequence.structure), function(x){
object[[sequence.structure[x]]]
})
object <- set_RLum(class = "RLum.Analysis", records = object, protocol = "pIRIR")
##(2) Perform pIRIR analysis (for this example with quartz OSL data!)
## Note: output as single plots to avoid problems with this example
results <- analyse_pIRIRSequence(object,
signal.integral.min = 1,
signal.integral.max = 2,
background.integral.min = 900,
background.integral.max = 1000,
fit.method = "EXP",
sequence.structure = c("TL", "pseudoIRSL1", "pseudoIRSL2"),
main = "Pseudo pIRIR data set based on quartz OSL",
plot.single = TRUE)
##(3) Perform pIRIR analysis (for this example with quartz OSL data!)
## Alternative for PDF output, uncomment and complete for usage
# }
# NOT RUN {
pdf(file = "...", height = 15, width = 15)
results <- analyse_pIRIRSequence(object,
signal.integral.min = 1,
signal.integral.max = 2,
background.integral.min = 900,
background.integral.max = 1000,
fit.method = "EXP",
main = "Pseudo pIRIR data set based on quartz OSL")
dev.off()
# }
# NOT RUN {
# }
```

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