‘BayLum’ provides a collection of various **R** functions for Bayesian analysis of luminescence data. Amongst others, this includes data import, export, application of age models and palaeodose modelling.

Data can be processed simultaneously for various samples, including the input of multiple BIN/BINX-files per sample for single grain (SG) or multigrain (MG) OSL measurements. Stratigraphic constraints and systematic errors can be added to constrain the analysis further.

For those who already know how to use **R**, ‘BayLum’ won’t be difficult to use, for all others, this brief introduction may be of help to make the first steps with **R** and the package ‘BayLum’ as convenient as possible.

If you read this document before having installed **R** itself, you should first visit the R project webpage and download and install **R**. You may also consider installing Rstudio, which provides an excellent desktop working environment for **R**; however it is not a prerequisite.

Despite, you will need the external software *JAGS* (Just Another Gibs Sampler). Please visit the JAGS webpage and follow the installation instructions. Now you are nearly ready to work with ‘BayLum’.

If you have not yet installed `BayLum’, please run the following two **R** code lines to install ‘BayLum’ on your computer.

Alternatively, you can load an already installed **R** package (here ‘BayLum’) into your session by using the following **R** call.

Let us consider the sample is named *samp1*, which is the example dataset coming with the package. All information related to this sample is stored in a subfolder called also *samp1*. To test the package example, first, we add the path of the example dataset to the object `path`

.

Please note that for your own dataset (i.e. not included in the package) you have to replace this call by something like:

In our example the folder contains the following subfolders and files:

1 | FER1/bin.BIN |

2 | FER1/Disc.csv |

3 | FER1/DoseEnv.csv |

4 | FER1/DoseSource.csv |

5 | FER1/rule.csv |

6 | samp1/bin.BIN |

7 | samp1/DiscPos.csv |

8 | samp1/DoseEnv.csv |

9 | samp1/DoseSource.csv |

10 | samp1/rule.csv |

11 | samp2/bin.BIN |

12 | samp2/DiscPos.csv |

13 | samp2/DoseEnv.csv |

14 | samp2/DoseSource.csv |

15 | samp2/rule.csv |

See *“What are the required files in each subfolder?”* in the manual of `Generate_DataFile()`

function for the meaning of these files.

To import your data, simply call the function `Generate_DataFile()`

:

The import may take a while, in particular for large BIN/BINX-files. This can become annoying if you want to play with the data. In such situations, it makes sense to save your imported data somewhere else before continuing.

To save the obove imported data on your hardrive use

To load the data use

To see the overall structure of the data generated from the BIN/BINX-file and the associated CSV-files, the following call can be used:

```
List of 9
$ LT :List of 1
..$ : num [1, 1:7] 2.042 0.842 1.678 3.826 4.258 ...
$ sLT :List of 1
..$ : num [1, 1:7] 0.344 0.162 0.328 0.803 0.941 ...
$ ITimes :List of 1
..$ : num [1, 1:6] 15 30 60 100 0 15
$ dLab : num [1:2, 1] 1.53e-01 5.89e-05
$ ddot_env : num [1:2, 1] 2.512 0.0563
$ regDose :List of 1
..$ : num [1, 1:6] 2.3 4.6 9.21 15.35 0 ...
$ J : num 1
$ K : num 6
$ Nb_measurement: num 16
```

It reveals that `DATA1`

is basically a list with 9 elements:

Element | Content |
---|---|

`DATA1$LT` |
Lx/Tx values from each sample |

`DATA1$sLT` |
Lx/Tx error values from each sample |

`DATA1$ITimes` |
Irradiation times |

`DATA1$dLab` |
The lab dose rate |

`DATA1$ddot_env` |
The environmental dose rate and its variance |

`DATA1$regDose` |
The regenarated dose points |

`DATA1$J` |
The number of aliquots selected for each BIN-file |

`DATA1$K` |
The number of regenarted dose points |

`DATA1$Nb_measurement` |
The number of measurements per BIN-file |

To get an impression on how your data look like, you can visualise them by using the function `LT_RegenDose()`

:

```
LT_RegenDose(
DATA = DATA1,
Path = path,
FolderNames = "samp1",
SampleNames = "samp1",
Nb_sample = 1,
nrow = NULL
)
```

Note that here we consider only one sample, and the name of the folder is the name of the sample. For that reason the argumetns were set to `FolderNames = samp1`

and `SampleNames = samp1`

.

For a multi-grain OSL measurements, instead of `Generate_DataFile()`

, the function `Generate_DataFile_MG()`

should be used with similar parameters. The functions differ by their expectations: *Disc.csv* instead of *DiscPos.csv* file for Single-grain OSL Measurements. Please check type `?Generate_DataFile_MG`

for further information.

To compute the age of the sample *samp1*, you can run the following code:

```
Age <- Age_Computation(
DATA = DATA1,
SampleName = "samp1",
PriorAge = c(10, 100),
distribution = "cauchy",
LIN_fit = TRUE,
Origin_fit = FALSE,
Iter = 10000
)
```

```
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 6
Unobserved stochastic nodes: 9
Total graph size: 139
Initializing model
```

```
>> Sample name <<
----------------------------------------------
samp1
>> Results of the Gelman and Rubin criterion of convergence <<
----------------------------------------------
Point estimate Uppers confidence interval
A 1.02 1.05
D 1.02 1.06
sD 1.08 1.12
---------------------------------------------------------------------------------------------------
*** WARNING: The following information are only valid if the MCMC chains have converged ***
---------------------------------------------------------------------------------------------------
parameter Bayes estimate Credible interval
----------------------------------------------
A 24.373
lower bound upper bound
at level 95% 10 67.99
at level 68% 10 24.49
----------------------------------------------
D 60.659
lower bound upper bound
at level 95% 20.37 169.95
at level 68% 22.02 61.34
----------------------------------------------
sD 39.715
lower bound upper bound
at level 95% 0.03 138.27
at level 68% 0.31 30.22
```

This also works if `DATA1`

is the output of `Generate_DataFile_MG()`

.

If MCMC trajectories did not converge, you can add more iteration with the parameter

`Iter`

in the function`Age_Computation()`

, for example`Iter = 20000`

or`Iter = 50000`

.To increase the precision of prior distribution, if not specified before you can use the argument

`PriorAge`

. For example:`PriorAge= c(0.01,10)`

for a young sample and`PriorAge = c(10,100)`

for an old sample.If the trajectories are still not convergering, you should whether the choice you made with the argument

`distribution`

and dose-response curves are meaningful.

`LIN_fit`

and `Origin_fit`

, dose-response curves option- By default, a saturating exponential plus linear dose response curve is expected. However, you choose other formula by changing arguments
`LIN_fit`

and`Origin_fit`

in the function.

`distribution`

, equivalent dose dispersion optionBy default, a *cauchy* distribution is assumed, but you can choose another distribution by replacing the word `cauchy`

by `gaussian`

, `lognormal_A`

or `lognormal_M`

for the argument `distribution`

.

The difference between the models: *lognormal_A* and *lognormal_M* is that the equivalent dose dispersion are distributed according to:

- a lognormal distribution with mean or average equal to the palaeodose for the first model
- a lognormal distribution with median equal to the palaeodose for the second model.

`SavePdf`

and `SaveEstimates`

optionThese two arguments allow to save the results to files.

`SavePdf = TRUE`

create a PDF-file with MCMC trajectories of parameters`A`

(age),`D`

(palaeodose),`sD`

(equivalent doses dispersion). You have to specify`OutputFileName`

and`OutputFilePath`

to define name and path of the PDF-file.`SaveEstimates = TRUE`

saves a CSV-file containing the Bayes estimates, the credible interval at 68% and 95% and the Gelman and Rudin test of convergency of the parameters`A`

,`D`

,`sD`

. For the export the arugments`OutputTableName`

and`OutputTablePath`

have to be specified.

`PriorAge`

optionBy default, an age between 0.01 ka and 100 ka is expected. If the user has more informations on the sample, `PriorAge`

should be modified accordingly.

For example, if you know that the sample is an older, you can set `PriorAge=c(10,120)`

. In contrast, if you know that the sample is younger, you may want to set `PriorAge=c(0.001,10)`

. Ages of \(<=0\) are not possible. The minimum bound is 0.001.

**Please note that the setting of PriorAge is not trivial, wrongly set boundaries are likely biasing your results.**

In the previous example we considered only the simplest case: one sample, and one BIN/BINX-file. However, ‘BayLum’ allows to process multiple BIN/BINX-files for one sample. To work with multiple BIN/BINX-files, the names of the subfolders need to beset in argument `Names`

and both files need to be located unter the same `Path`

.

For the case

the call `Generate_DataFile()`

(or `Generate_DataFile_MG()`

) becomes as follows:

```
##argument setting
nbsample <- 1
nbbinfile <- length(Names)
Binpersample <- c(length(Names))
##call data file generator
DATA_BF <- Generate_DataFile(
Path = path,
FolderNames = Names,
Nb_sample = nbsample,
Nb_binfile = nbbinfile,
BinPerSample = Binpersample,
verbose = FALSE
)
##calculate the age
Age <- Age_Computation(
DATA = DATA_BF,
SampleName = Names,
BinPerSample = Binpersample
)
```

```
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 12
Unobserved stochastic nodes: 15
Total graph size: 221
Initializing model
```

```
>> Sample name <<
----------------------------------------------
samp1 samp2
>> Results of the Gelman and Rubin criterion of convergence <<
----------------------------------------------
Point estimate Uppers confidence interval
A 1.13 1.26
D 1.14 1.29
sD 1.27 1.75
---------------------------------------------------------------------------------------------------
*** WARNING: The following information are only valid if the MCMC chains have converged ***
---------------------------------------------------------------------------------------------------
parameter Bayes estimate Credible interval
----------------------------------------------
A 2.364
lower bound upper bound
at level 95% 1.08 3.38
at level 68% 1.71 2.7
----------------------------------------------
D 5.876
lower bound upper bound
at level 95% 2.88 8.18
at level 68% 4.39 6.7
----------------------------------------------
sD 1.123
lower bound upper bound
at level 95% 0 2.43
at level 68% 0 0.75
```

The function `Generate_DataFile()`

(or `Generate_DataFile_MF()`

) can process multiple files simultaneously including multiple BIN/BINX-files per sample.

We assume that we are interested in two samples named: *sample1* and *sample2*. In addition, we have two BIN/BINX-files for the first sample named: *sample1-1* and *sample1-2*, and one BIN-file for the 2nd sample named *sample2-1*. In such case, we need three subfolders named *sample1-1*, *sample1-2* and *sample2-1*; which each subfolder containing only one BIN-file named **bin.BIN**, and its associated files **DiscPos.csv**, **DoseEnv.csv**, **DoseSourve.csv** and **rule.csv**. All of these 3 subfolders must be located in *path*.

To fill the argument corectly `BinPerSample`

: \(binpersample=c(\underbrace{2}_{\text{sample 1: 2 bin files}},\underbrace{1}_{\text{sample 2: 1 bin file}})\)

```
Names <-
c("sample1-1", "sample1-2", "sample2-1") # give the name of the folder datat
nbsample <- 2 # give the number of samples
nbbinfile <- 3 # give the number of bin files
DATA <- Generate_DataFile(
Path = path,
FolderNames = Names,
Nb_sample = nbsample,
Nb_binfile = nbbinfile,
BinPerSample = binpersample
)
```

`combine_DataFiles()`

If the user has already saved informations imported with `Generate_DataFile()`

function (or `Generate_DataFile_MG()`

function) these data can be concatenate with the function `combine_DataFiles()`

.

For example, if `DATA1`

is the output of sample named “GDB3”, and `DATA2`

is the output of sample “GDB5”, both data can be merged with the following call:

```
data("DATA1", envir = environment())
data("DATA2", envir = environment())
DATA3 <- combine_DataFiles(L1 = DATA2, L2 = DATA1)
str(DATA3)
```

```
List of 9
$ LT :List of 2
..$ : num [1:188, 1:6] 4.54 2.73 2.54 2.27 1.48 ...
..$ : num [1:101, 1:6] 5.66 6.9 4.05 3.43 4.97 ...
$ sLT :List of 2
..$ : num [1:188, 1:6] 0.333 0.386 0.128 0.171 0.145 ...
..$ : num [1:101, 1:6] 0.373 0.315 0.245 0.181 0.246 ...
$ ITimes :List of 2
..$ : num [1:188, 1:5] 40 40 40 40 40 40 40 40 40 40 ...
..$ : num [1:101, 1:5] 160 160 160 160 160 160 160 160 160 160 ...
$ dLab : num [1:2, 1:2] 1.53e-01 5.89e-05 1.53e-01 5.89e-05
$ ddot_env : num [1:2, 1:2] 2.512 0.0563 2.26 0.0617
$ regDose :List of 2
..$ : num [1:188, 1:5] 6.14 6.14 6.14 6.14 6.14 6.14 6.14 6.14 6.14 6.14 ...
..$ : num [1:101, 1:5] 24.6 24.6 24.6 24.6 24.6 ...
$ J : num [1:2] 188 101
$ K : num [1:2] 5 5
$ Nb_measurement: num [1:2] 14 14
```

The data structure should become as follows

- 2
`list`

s (1`list`

per sample) for`DATA$LT`

,`DATA$sLT`

,`DATA1$ITimes`

and`DATA1$regDose`

- A
`matrix`

with 2 columns (1 line per sample) for`DATA1$dLab`

,`DATA1$ddot_env`

- 2
`integer`

s (1`integer`

per BIN files here we have 1 BIN-file per sample) for`DATA1$J`

,`DATA1$K`

,`DATA1$Nb_measurement`

.

Single-grain and multiple-grain OSL measurements can be merged in the same way. To plot the \(L/T\) as a function of the regenerative dose the function `LT_RegenDose()`

can be used again:

```
LT_RegenDose(
DATA = DATA3,
Path = path,
FolderNames = Names,
Nb_sample = nbsample,
SG = rep(TRUE, nbsample)
)
```

*Note: In the example DATA3 contains information from the samples ‘GDB3’ and ‘GDB5’, which are single-grain OSL measurements. For a correct treatment the argument SG has to be manually set be the user. Please see the function manual for further details.*

If there no stratigraphic constraints were set, the following code to analyse simultaneously the age of the sample *GDB5* and *GDB3*.

```
priorage = c(1, 10, 10, 100)
Age <- AgeS_Computation(
DATA = DATA3,
Nb_sample = 2,
SampleNames = c("GDB5", "GDB3"),
PriorAge = priorage,
distribution = "cauchy",
LIN_fit = TRUE,
Origin_fit = FALSE,
Iter = 1000
)
```

```
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1445
Unobserved stochastic nodes: 1739
Total graph size: 20624
Initializing model
```

`Warning: [plot_MCMC()] 'n.iter' out of range, reset to number of observations`

```
>> Results of the Gelman and Rubin criterion of convergence <<
----------------------------------------------
Sample name: GDB5
---------------------
Point estimate Uppers confidence interval
A_GDB5 1 1.01
D_GDB5 1 1.01
sD_GDB5 1.01 1.03
----------------------------------------------
Sample name: GDB3
---------------------
Point estimate Uppers confidence interval
A_GDB3 1 1
D_GDB3 1.01 1.03
sD_GDB3 1 1
---------------------------------------------------------------------------------------------------
*** WARNING: The following information are only valid if the MCMC chains have converged ***
---------------------------------------------------------------------------------------------------
>> Bayes estimates of Age, Palaeodose and its dispersion for each sample and credible interval <<
----------------------------------------------
Sample name: GDB5
---------------------
Parameter Bayes estimate Credible interval
A_GDB5 7.108
lower bound upper bound
at level 95% 5.71 8.35
at level 68% 6.36 7.76
Parameter Bayes estimate Credible interval
D_GDB5 17.696
lower bound upper bound
at level 95% 16.6 18.9
at level 68% 17.22 18.31
Parameter Bayes estimate Credible interval
sD_GDB5 4.384
lower bound upper bound
at level 95% 3.52 5.46
at level 68% 3.95 4.94
----------------------------------------------
Sample name: GDB3
---------------------
Parameter Bayes estimate Credible interval
A_GDB3 46.728
lower bound upper bound
at level 95% 37.06 57.57
at level 68% 39.86 50.04
Parameter Bayes estimate Credible interval
D_GDB3 104.739
lower bound upper bound
at level 95% 98.5 112.54
at level 68% 101 108.03
Parameter Bayes estimate Credible interval
sD_GDB3 15.522
lower bound upper bound
at level 95% 9.68 21.13
at level 68% 11.94 17.73
----------------------------------------------
```

If the MCMC trajectories did not converge, we refer to the comments above.

As for the function `Age_computation()`

, the age for each sample is set by default between 0.01 ka and 100 ka. If you have more informations on your samples it is possible to change `PriorAge`

parameters. `PriorAge`

is a vector of `size = 2*$Nb_sample`

, the two first values of `PriorAge`

concern the 1st sample, the next two values the 2nd sample and so on.

For example, if you know that sample named *GDB5* is a young sample whose its age is between 0.01 ka and 10 ka, and *GDB3* is an old sample whose age is between 10 ka and 100 ka, \[PriorAge=c(\underbrace{0.01,10}_{GDB5\ prior\ age},\underbrace{10,100}_{GDB3\ prior\ age})\]

With the function `AgeS_Computation()`

it is possible to take the stratigraphic relations between samples into account and define constraints.

For example, we know that *GDB5* is in a higher stratigraphical position, hence it likely has a younger age than sample *GDB3*.

To take into account stratigraphic constraints, the information on the samples need to be ordered. Either you enter a sample name (corresponding to subfolder names) in `Names`

parameter of the function `Generate_DataFile()`

, ordered by order of increasing ages or you enter saved .RData informations of each sample in `combine_DataFiles()`

, ordered by increasing ages.

Let `SC`

be the matrix containing all information on stratigraphic relations for this two samples. This matrix is defined as follows:

matrix dimensions: the row number of

`StratiConstraints`

matrix is equal to`Nb_sample+1`

, and column number is equal to \(Nb\_sample\).first matrix row: for all \(i\) in \(\{1,...,Nb\_Sample\}\),

`StratiConstraints[1,i] <- 1`

, means that the lower bound of the sample age given in`PriorAge[2i-1]`

for the sample whose number ID is equal to \(i\) is taken into accountsample relations: for all \(j\) in ${2,…,Nb_Sample+1}$ and all \(i\) in \(\{j,...,Nb\_Sample\}\),

`StratiConstraints[j,i] <- 1`

if the sample age whose ID is equal to \(j-1\) is lower than the sample age whose ID is equal to \(i\). Otherwise,`StratiConstraints[j,i] <- 0`

.

To the define such matrix the function *SCMatrix()* can be used:

In our case: 2 samples, `SC`

is a matrix with 3 rows and 2 columns. The first row contains `c(1,1)`

(because we take into account the prior ages), the second line contains `c(0,1)`

(sample 2, named *samp2* is supposed to be older than sample 1, named *samp1*) and the third line contains `c(0,0)`

(sample 2, named *samp2* is not younger than the sample 1, here named *samp1*). We can also fill the matrix with the stratigraphic relations as follow:

```
Age <-
AgeS_Computation(
DATA = DATA3,
Nb_sample = 2,
SampleNames = c("samp1", "samp2"),
PriorAge = priorage,
distribution = "cauchy",
LIN_fit = TRUE,
Origin_fit = FALSE,
StratiConstraints = SC,
Iter = 1000
)
```

```
Compiling model graph
Resolving undeclared variables
Allocating nodes
Graph information:
Observed stochastic nodes: 1445
Unobserved stochastic nodes: 1739
Total graph size: 20624
Initializing model
```

`Warning: [plot_MCMC()] 'n.iter' out of range, reset to number of observations`

```
>> Results of the Gelman and Rubin criterion of convergence <<
----------------------------------------------
Sample name: samp1
---------------------
Point estimate Uppers confidence interval
A_samp1 1.02 1.04
D_samp1 1.01 1.03
sD_samp1 1 1.02
----------------------------------------------
Sample name: samp2
---------------------
Point estimate Uppers confidence interval
A_samp2 1.02 1.03
D_samp2 1 1
sD_samp2 1.03 1.09
---------------------------------------------------------------------------------------------------
*** WARNING: The following information are only valid if the MCMC chains have converged ***
---------------------------------------------------------------------------------------------------
>> Bayes estimates of Age, Palaeodose and its dispersion for each sample and credible interval <<
----------------------------------------------
Sample name: samp1
---------------------
Parameter Bayes estimate Credible interval
A_samp1 9.709
lower bound upper bound
at level 95% 9.14 10
at level 68% 9.67 10
Parameter Bayes estimate Credible interval
D_samp1 29.14
lower bound upper bound
at level 95% 24.15 33.88
at level 68% 27.04 31.98
Parameter Bayes estimate Credible interval
sD_samp1 68.34
lower bound upper bound
at level 95% 51.4 87.58
at level 68% 59.34 78
----------------------------------------------
Sample name: samp2
---------------------
Parameter Bayes estimate Credible interval
A_samp2 10.39
lower bound upper bound
at level 95% 10 11.24
at level 68% 10 10.43
Parameter Bayes estimate Credible interval
D_samp2 18.26
lower bound upper bound
at level 95% 17.11 19.3
at level 68% 17.56 18.78
Parameter Bayes estimate Credible interval
sD_samp2 4.595
lower bound upper bound
at level 95% 3.49 5.5
at level 68% 3.96 4.92
----------------------------------------------
```

Combès, B., Philippe, A., Lanos, P., Mercier, N., Tribolo, C., Guerin, G., Guibert, P., Lahaye, C., 2015. A Bayesian central equivalent dose model for optically stimulated luminescence dating. Quaternary Geochronology 28, 62-70. doi: 10.1016/j.quageo.2015.04.001

Combès, B., Philippe, A., 2017. Bayesian analysis of individual and systematic multiplicative errors for estimating ages with stratigraphic constraints in optically stimulated luminescence dating. Quaternary Geochronology 39, 24–34. doi: 10.1016/j.quageo.2017.02.003

Philippe, A., Guérin, G., Kreutzer, S., in press. BayLum - An R package for Bayesian analysis of OSL ages: An introduction. Quaternary Geochronology. doi: 10.1016/j.quageo.2018.05.009

Robert and Casella, 2009. Introducing Monte Carlo Methods with R. Springer Science & Business Media.

Tribolo, C., Asrat, A., Bahain, J. J., Chapon, C., Douville, E., Fragnol, C., Hernandez, M., Hovers, E., Leplongeon, A., Martin, L., Pleurdeau, D., Pearson, O., Puaud, S., Assefa, Z., 2017. Across the Gap: Geochronological and Sedimentological Analyses from the Late Pleistocene-Holocene Sequence of Goda Buticha, Southeastern Ethiopia. PloS one, 12(1), e0169418. doi: 10.1371/journal.pone.0169418