diff --git a/.zenodo.json b/.zenodo.json
index 4650f06c..356209f5 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -39,6 +39,6 @@
],
"license": "GPL-3.0+",
"access_right": "open",
- "version": "0.3.2.9000-59",
+ "version": "0.3.2.9000-61",
"publication_date": "2024-03-16"
}
diff --git a/BayLum.BuildResults/BayLum-Ex.timings.0.3.2.9000-59.WARNING b/BayLum.BuildResults/BayLum-Ex.timings.0.3.2.9000-61.WARNING
similarity index 100%
rename from BayLum.BuildResults/BayLum-Ex.timings.0.3.2.9000-59.WARNING
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similarity index 75%
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diff --git a/BayLum.BuildResults/BayLum_0.3.2.9000-59-Functions.csv b/BayLum.BuildResults/BayLum_0.3.2.9000-61-Functions.csv
similarity index 94%
rename from BayLum.BuildResults/BayLum_0.3.2.9000-59-Functions.csv
rename to BayLum.BuildResults/BayLum_0.3.2.9000-61-Functions.csv
index 53f5362a..55f73fa2 100644
--- a/BayLum.BuildResults/BayLum_0.3.2.9000-59-Functions.csv
+++ b/BayLum.BuildResults/BayLum_0.3.2.9000-61-Functions.csv
@@ -1,37 +1,37 @@
"Name","Title","Description","Version","m.Date","m.Time","Author","Citation"
-"Age_Computation","Bayesian analysis for the OSL age estimation of one sample","This function computes the age (in ka) of a sample according to the model developed in Combes and Philippe (2017), based on an output of Generate_DataFile or Generate_DataFile_MG . A sample, for which data is available in several BIN files, can be analysed.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin
","Christophe, C., Kreutzer, S., Philippe, A., Guérin, G., 2024. Age_Computation(): Bayesian analysis for the OSL age estimation of one sample. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"Age_Computation","Bayesian analysis for the OSL age estimation of one sample","This function computes the age (in ka) of a sample according to the model developed in Combes and Philippe (2017), based on an output of Generate_DataFile or Generate_DataFile_MG . A sample, for which data is available in several BIN files, can be analysed.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin
","Christophe, C., Kreutzer, S., Philippe, A., Guérin, G., 2024. Age_Computation(): Bayesian analysis for the OSL age estimation of one sample. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
-"Age_OSLC14","Bayesian analysis for age estimation of OSL measurements and C-14 ages of various samples","This function computes an age of OSL data consisting of at least two samples and calibrate C-14 ages of samples to get an age (in ka). Ages of OSL data are computed according to the model given in Combes and Philippe (2017). Single-grain or Multi-grain OSL measurements can be analysed simultaneously (with output of Generate_DataFile or Generate_DataFile_MG or both of them using combine_DataFiles ). Samples, for which data is available in several BIN files, can be analysed. For C-14 data, the user can choose one of the following radiocarbon calibration curve: Northern or Southern Hemisphere or marine atmospheric.",NA,NA,NA,"Claire Christophe, Anne Philippe, Guillaume Guerin, Sebastian Kreutzer, Frederik Harly Baumgarten
","Christophe, C., Philippe, A., Kreutzer, S., Baumgarten, F.H., 2024. Age_OSLC14(): Bayesian analysis for age estimation of OSL measurements and C-14 ages of various samples. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"Age_OSLC14","Bayesian analysis for age estimation of OSL measurements and C-14 ages of various samples","This function computes an age of OSL data consisting of at least two samples and calibrate C-14 ages of samples to get an age (in ka). Ages of OSL data are computed according to the model given in Combes and Philippe (2017). Single-grain or Multi-grain OSL measurements can be analysed simultaneously (with output of Generate_DataFile or Generate_DataFile_MG or both of them using combine_DataFiles ). Samples, for which data is available in several BIN files, can be analysed. For C-14 data, the user can choose one of the following radiocarbon calibration curve: Northern or Southern Hemisphere or marine atmospheric.",NA,NA,NA,"Claire Christophe, Anne Philippe, Guillaume Guerin, Sebastian Kreutzer, Frederik Harly Baumgarten
","Christophe, C., Philippe, A., Kreutzer, S., Baumgarten, F.H., 2024. Age_OSLC14(): Bayesian analysis for age estimation of OSL measurements and C-14 ages of various samples. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
-"AgeC14_Computation","Bayesian analysis for C-14 age estimations of various samples","This function calibrates the C-14 age of samples to get an age (in ka). The user can choose one of the following radiocarbon calibration curve: Northern or Southern Hemisphere or marine atmospheric. It must be the same curve for all samples.",NA,NA,NA,"Claire Christophe, Anne Philippe, Guillaume Guérin, Sebastian Kreutzer
","Christophe, C., Philippe, A., Guérin, G., Kreutzer, S., 2024. AgeC14_Computation(): Bayesian analysis for C-14 age estimations of various samples. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"AgeC14_Computation","Bayesian analysis for C-14 age estimations of various samples","This function calibrates the C-14 age of samples to get an age (in ka). The user can choose one of the following radiocarbon calibration curve: Northern or Southern Hemisphere or marine atmospheric. It must be the same curve for all samples.",NA,NA,NA,"Claire Christophe, Anne Philippe, Guillaume Guérin, Sebastian Kreutzer
","Christophe, C., Philippe, A., Guérin, G., Kreutzer, S., 2024. AgeC14_Computation(): Bayesian analysis for C-14 age estimations of various samples. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
-"AgeS_Computation","Bayesian analysis for OSL age estimation of various samples","This function computes the age (in ka) of at least two samples according to the model developed in Combès and Philippe (2017), based on outputs of Generate_DataFile or Generate_DataFile_MG or both of them using combine_DataFiles . Samples, for which data is available in several BIN files, can be analysed. Single-grain or Multi-grain OSL measurements can be analysed simultaneously.",NA,NA,NA,"Claire Christophe, Anne Philippe, Guillaume Guérin, Sebastian Kreutzer
","Christophe, C., Philippe, A., Guérin, G., Kreutzer, S., 2024. AgeS_Computation(): Bayesian analysis for OSL age estimation of various samples. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"AgeS_Computation","Bayesian analysis for OSL age estimation of various samples","This function computes the age (in ka) of at least two samples according to the model developed in Combès and Philippe (2017), based on outputs of Generate_DataFile or Generate_DataFile_MG or both of them using combine_DataFiles . Samples, for which data is available in several BIN files, can be analysed. Single-grain or Multi-grain OSL measurements can be analysed simultaneously.",NA,NA,NA,"Claire Christophe, Anne Philippe, Guillaume Guérin, Sebastian Kreutzer
","Christophe, C., Philippe, A., Guérin, G., Kreutzer, S., 2024. AgeS_Computation(): Bayesian analysis for OSL age estimation of various samples. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"AgeS","Output of AgeS_Computation function for the samples: \"GDB5\" and \"GDB3\"
","Output of AgeS_Computation function for the samples: \"GDB5\" and \"GDB3\", there is no stratigraphic relation neither systematic errors.",NA,NA,NA,NA,NA
"BayLum-deprecated","Deprecated functions in package BayLum .","The functions listed below are deprecated and will be defunct in the near future. When possible, alternative functions with similar functionality are also mentioned. Help pages for deprecated functions are available at help(\"-deprecated\") .",NA,NA,NA,NA,NA
"combine_DataFiles","Combine objects","Combine objects generated by Generate_DataFile and Generate_DataFile_MG","0.1.1
-",NA,NA,"Sebastian Kreutzer, IRAMAT-CRP2A, UMR 5060, CNRS - Université Bordeaux Montaigne (France), adapting
the idea from the function 'Concat_DataFile()' by Claire Christophe.
","Kreutzer, S., Christophe, C., 2024. combine_DataFiles(): Combine objects. Function version 0.1.1. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+",NA,NA,"Sebastian Kreutzer, IRAMAT-CRP2A, UMR 5060, CNRS - Université Bordeaux Montaigne (France), adapting
the idea from the function 'Concat_DataFile()' by Claire Christophe.
","Kreutzer, S., Christophe, C., 2024. combine_DataFiles(): Combine objects. Function version 0.1.1. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"create_DataFile","Prepare input data for subsequent BayLum Analysis","The function pre-processes input data from BIN/BINX file, XSYG files or RLum.Analysis objects for 'BayLum' . The parameters for the modelling are controlled by a to be supplied YAML configuration file (please read package vignette).","0.1.0
-",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl University of Heidelberg (Germany), in parts based on code by Claire Christophe
","Kreutzer, S., Christophe, C., 2024. create_DataFile(): Prepare input data for subsequent BayLum Analysis. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl University of Heidelberg (Germany), in parts based on code by Claire Christophe
","Kreutzer, S., Christophe, C., 2024. create_DataFile(): Prepare input data for subsequent BayLum Analysis. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"create_FolderTemplates","Create Folder Templates","Create file and folder structure templates on the user hard drive as expected by Generate_DataFile and Generate_DataFile_MG . Files and data in the folders must then be overwritten manually with user data. The function intends to minimise the errors going along with the creation of these folder structures. The function uses the example data of BayLum to create the templates.","0.1.0
-",NA,NA,"Sebastian Kreutzer, Geography & Earth Sciences, Aberystwyth University
(United Kingdom)
","Kreutzer, S., 2024. create_FolderTemplates(): Create Folder Templates. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+",NA,NA,"Sebastian Kreutzer, Geography & Earth Sciences, Aberystwyth University
(United Kingdom)
","Kreutzer, S., 2024. create_FolderTemplates(): Create Folder Templates. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"create_ThetaMatrix","Create Theta Matrix","Create the \Theta matrix with the shared uncertainties that can used as input in, e.g., AgeS_Computation and Age_OSLC14 which is used for the covariance matrix \Sigma (Combès & Philippe, 2017)","0.1.0
-",NA,NA,"Sebastian Kreutzer, IRAMAT-CRP2A, UMR 5060, CNRS-Université Bordeaux Montaigne (France), based
on an 'MS Excel' sheet by Guillaume Guérin, IRAMAT-CRP2A, UMR 5060, CNRS-Université Bordeaux Montaigne (France)
","Kreutzer, S., Guérin, G., 2024. create_ThetaMatrix(): Create Theta Matrix. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+",NA,NA,"Sebastian Kreutzer, IRAMAT-CRP2A, UMR 5060, CNRS-Université Bordeaux Montaigne (France), based
on an 'MS Excel' sheet by Guillaume Guérin, IRAMAT-CRP2A, UMR 5060, CNRS-Université Bordeaux Montaigne (France)
","Kreutzer, S., Guérin, G., 2024. create_ThetaMatrix(): Create Theta Matrix. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"DATA_C14","C14 cal age estiamte and its error
","C14 cal age estiamtes and theirs error of samples S-EVA-26510, S-EVA-26506, S-EVA-26507, S-EVA-26508.",NA,NA,NA,NA,NA
"DATA1","DATA of sample named GDB3
%% ~~ data name/kind ... ~~
","list of objects: LT, sLT, ITimes, dLab, ddot_env, regDose, J,K,Nb_measurement obtained using Generate_DataFile function with single-grain OSL measurementsl of the sample GDB3. %% ~~ A concise (1-5 lines) description of the dataset. ~~",NA,NA,NA,NA,NA
"DATA2","DATA on sample named GDB5
%% ~~ data name/kind ... ~~
","list of objects: LT, sLT, ITimes, dLab, ddot_env, regDose, J,K,Nb_measurement obtained using Generate_DataFile function with single-grain OSL measurementsl of the sample GDB5. %% ~~ A concise (1-5 lines) description of the dataset. ~~",NA,NA,NA,NA,NA
"DATA3","
DATA of sample named FER1","list of objects: LT, sLT, ITimes, dLab, ddot_env, regDose, J,K,Nb_measurement obtained using Generate_DataFile function with multi-grain OSL measurementsl of the sample FER1. %% ~~ A concise (1-5 lines) description of the dataset. ~~",NA,NA,NA,NA,NA
-"Generate_DataFile_MG-deprecated","Generates, from one (or several) BIN file(s) of Multi-grain OSL measurements a list of luminescence data and information before statistical analysis (DEPRECATED)","This function is used to generate, from the BIN file(s), a list of values of: Multi-grain OSL intensities and associated uncertainties, regenerative doses, etc., which will be the input of the Bayesian models. To be easy-to-use, this function requires a rigorous organisation - all needed files should be arranged in one folder - of informations concerning each BIN file. It is possible to process data for various samples simultaneously and to consider more than one BIN-file per sample.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin
","Christophe, C., Kreutzer, S., Philippe, A., Guérin, G., 2024. Generate_DataFile_MG-deprecated(): Generates, from one (or several) BIN file(s) of Multi-grain OSL measurements a list of luminescence data and information before statistical analysis (DEPRECATED). In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"Generate_DataFile_MG-deprecated","Generates, from one (or several) BIN file(s) of Multi-grain OSL measurements a list of luminescence data and information before statistical analysis (DEPRECATED)","This function is used to generate, from the BIN file(s), a list of values of: Multi-grain OSL intensities and associated uncertainties, regenerative doses, etc., which will be the input of the Bayesian models. To be easy-to-use, this function requires a rigorous organisation - all needed files should be arranged in one folder - of informations concerning each BIN file. It is possible to process data for various samples simultaneously and to consider more than one BIN-file per sample.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin
","Christophe, C., Kreutzer, S., Philippe, A., Guérin, G., 2024. Generate_DataFile_MG-deprecated(): Generates, from one (or several) BIN file(s) of Multi-grain OSL measurements a list of luminescence data and information before statistical analysis (DEPRECATED). In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
-"Generate_DataFile-deprecated","Generates, from one (or several) BIN-file(s) of Single-grain OSL measurements, a list of luminescence data and information before statistical analysis (DEPRECATED)","This function is used to generate, from the BIN file(s), a list of values of: Single-grain OSL intensities and associated uncertainties, regenerative doses, etc., which will be the input of the Bayesian models. To be easy-to-use, this function requires a rigorous organisation - all needed files should be arranged in one folder - of informations concerning each BIN file. It is possible to process data for various samples simultaneously and to consider more than one BIN file per sample.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guerin
","Christophe, C., Kreutzer, S., Philippe, A., 2024. Generate_DataFile-deprecated(): Generates, from one (or several) BIN-file(s) of Single-grain OSL measurements, a list of luminescence data and information before statistical analysis (DEPRECATED). In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"Generate_DataFile-deprecated","Generates, from one (or several) BIN-file(s) of Single-grain OSL measurements, a list of luminescence data and information before statistical analysis (DEPRECATED)","This function is used to generate, from the BIN file(s), a list of values of: Single-grain OSL intensities and associated uncertainties, regenerative doses, etc., which will be the input of the Bayesian models. To be easy-to-use, this function requires a rigorous organisation - all needed files should be arranged in one folder - of informations concerning each BIN file. It is possible to process data for various samples simultaneously and to consider more than one BIN file per sample.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guerin
","Christophe, C., Kreutzer, S., Philippe, A., 2024. Generate_DataFile-deprecated(): Generates, from one (or several) BIN-file(s) of Single-grain OSL measurements, a list of luminescence data and information before statistical analysis (DEPRECATED). In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"IntCal13","
Atmospheric North data for calibration of 14C age
","As 14C years is not equal to calendar years because atmospheric 14C concentration varies through time. Hence, data in AtmosphericNorth_CalC14 allows a calibration for mid-latitude Northern Hemisphere atmospher reservoir.",NA,NA,NA,NA,NA
"IntCal20","
Atmospheric North data for calibration of 14C age
","As 14C years is not equal to calendar years because atmospheric 14C concentration varies through time. Hence, data in AtmosphericNorth_CalC14 allows a calibration for mid-latitude Northern Hemisphere atmospher reservoir.",NA,NA,NA,NA,NA
-"LT_RegenDose-deprecated","Plots Lx/Tx as a function of the regenerative dose (DEPRECATED)","This function plots Lx/Tx values as a function of regenerative dose, for every selected aliquot and for each sample.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin
","Christophe, C., Kreutzer, S., Philippe, A., Guérin, G., 2024. LT_RegenDose-deprecated(): Plots Lx/Tx as a function of the regenerative dose (DEPRECATED). In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"LT_RegenDose-deprecated","Plots Lx/Tx as a function of the regenerative dose (DEPRECATED)","This function plots Lx/Tx values as a function of regenerative dose, for every selected aliquot and for each sample.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin
","Christophe, C., Kreutzer, S., Philippe, A., Guérin, G., 2024. LT_RegenDose-deprecated(): Plots Lx/Tx as a function of the regenerative dose (DEPRECATED). In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"Marine13","
Marine data for calibration of 14C age ","As 14C years is not equal to calendar years because atmospheric 14C concentration varies through time. Hence, data in marine_CalC14 allows a calibration for hypothetical \"global\" marine reservoir.",NA,NA,NA,NA,NA
"Marine20","
Marine data for calibration of 14C age ","As 14C years is not equal to calendar years because atmospheric 14C concentration varies through time. Hence, data in marine_CalC14 allows a calibration for hypothetical \"global\" marine reservoir.",NA,NA,NA,NA,NA
@@ -43,28 +43,28 @@
"ModelC14","
Likelihood of C14 samples for JAGS models use in Age_OSLC14
","A list of models for C14 data to define likelyhood in JAGS models.",NA,NA,NA,NA,NA
"ModelOSL","
Likelihood of OSL samples for JAGS models use in Age_OSLC14
","A list of models for OSL data to define likelyhood in JAGS models.",NA,NA,NA,NA,NA
"ModelPrior","
Prior for JAGS models use in Age_OSLC14
","A list to define prior in JAGS models, taking acount OSL data and C14 data in stratigraphic constraint. The difficulty is in the fact that each cases is different. The youngest sample can be a C14 as well as a OSL sample. To resolve this problem we consider diferent cases thanks to this list.",NA,NA,NA,NA,NA
-"Palaeodose_Computation","Bayesian analysis for the palaeodose estimation of various samples","This function computes the palaeodose (in Gy) of one or various samples according to the model developed in Combes et al (2015), based on an output of Generate_DataFile or Generate_DataFile_MG or both of them using combine_DataFiles . Samples, for which data is avalilable in several BIN files, can be analysed. Single-grain or Multi-grain OSL measurements can be analysed simultaneouly.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin
","Christophe, C., Kreutzer, S., Philippe, A., Guérin, G., 2024. Palaeodose_Computation(): Bayesian analysis for the palaeodose estimation of various samples. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"Palaeodose_Computation","Bayesian analysis for the palaeodose estimation of various samples","This function computes the palaeodose (in Gy) of one or various samples according to the model developed in Combes et al (2015), based on an output of Generate_DataFile or Generate_DataFile_MG or both of them using combine_DataFiles . Samples, for which data is avalilable in several BIN files, can be analysed. Single-grain or Multi-grain OSL measurements can be analysed simultaneouly.",NA,NA,NA,"Claire Christophe, Sebastian Kreutzer, Anne Philippe, Guillaume Guérin
","Christophe, C., Kreutzer, S., Philippe, A., Guérin, G., 2024. Palaeodose_Computation(): Bayesian analysis for the palaeodose estimation of various samples. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"plot_Ages","Create Age Plot","Create Age Plot","0.1.5
-",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl-University of Heidelberg (Germany), based on code
written by Claire Christophe
","Kreutzer, S., Christophe, C., 2024. plot_Ages(): Create Age Plot. Function version 0.1.5. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl-University of Heidelberg (Germany), based on code
written by Claire Christophe
","Kreutzer, S., Christophe, C., 2024. plot_Ages(): Create Age Plot. Function version 0.1.5. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"plot_MCMC","Plot MCMC trajectories and posterior distributions","This function uses the output of rjags::jags.model to visualise the traces of the MCMC and the corresponding densities. In particular it displays the posterior distributions of the age, if it is calculated, palaeodose and the equivalent dose dispersion parameters of the sample. The function output is very similar to plot output produced with the 'coda' package, but tailored to meet the needs in the context of the 'BayLum' package.","0.1.5
-",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl University of Heidelberg (Germany). This function
is a re-written version of the function 'MCMC_plot()' by Claire Christophe
","Kreutzer, S., Christophe, C., 2024. plot_MCMC(): Plot MCMC trajectories and posterior distributions. Function version 0.1.5. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl University of Heidelberg (Germany). This function
is a re-written version of the function 'MCMC_plot()' by Claire Christophe
","Kreutzer, S., Christophe, C., 2024. plot_MCMC(): Plot MCMC trajectories and posterior distributions. Function version 0.1.5. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
-"plot_RegDosePoints","Plot Regeneration Dose Points","Simple plot functionality to visualise $L_x/T_x$ values against the dose extracted from data created by create_DataFile",NA,NA,NA,"Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany)
","Kreutzer, S., 2024. plot_RegDosePoints(): Plot Regeneration Dose Points. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"plot_RegDosePoints","Plot Regeneration Dose Points","Simple plot functionality to visualise $L_x/T_x$ values against the dose extracted from data created by create_DataFile",NA,NA,NA,"Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany)
","Kreutzer, S., 2024. plot_RegDosePoints(): Plot Regeneration Dose Points. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"plot_Scatterplots","Display Scatter Plot Matrix of the Bayesian Age Results","Create a hexbin plot matrix ( hexbin::hexplom ) of age results returned by the Bayesian age calculation.","0.3.2
-",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl University of Heidelberg (Germany) ,
based on the function 'ScatterSamples()' by Claire Christophe, Anne Philippe, Guillaume Guérin
","Kreutzer, S., Christophe, C., Philippe, A., Guérin, G., 2024. plot_Scatterplots(): Display Scatter Plot Matrix of the Bayesian Age Results. Function version 0.3.2. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl University of Heidelberg (Germany) ,
based on the function 'ScatterSamples()' by Claire Christophe, Anne Philippe, Guillaume Guérin
","Kreutzer, S., Christophe, C., Philippe, A., Guérin, G., 2024. plot_Scatterplots(): Display Scatter Plot Matrix of the Bayesian Age Results. Function version 0.3.2. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
-"SC_Ordered","Create Stratigraphically Ordered Sample Matrix","Construct the stratigraphic matrix used in the functions AgeS_Computation and AgeC14_Computation for samples that are all ordered by increasing age.",NA,NA,NA,"Claire Christophe, Anne Philippe, Sebastian Kreutzer, Guillaume Guérin
","Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., 2024. SC_Ordered(): Create Stratigraphically Ordered Sample Matrix. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"SC_Ordered","Create Stratigraphically Ordered Sample Matrix","Construct the stratigraphic matrix used in the functions AgeS_Computation and AgeC14_Computation for samples that are all ordered by increasing age.",NA,NA,NA,"Claire Christophe, Anne Philippe, Sebastian Kreutzer, Guillaume Guérin
","Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., 2024. SC_Ordered(): Create Stratigraphically Ordered Sample Matrix. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
-"SCMatrix","Construct the Stratigraphic Constrain Matrix Interactively","This function helps to define the stratigraphic relation between samples using questions. The output of this function can be used in the function AgeS_Computation .",NA,NA,NA,"Claire Christophe, Anne Philippe, Guillaume Guérin, Sebastian Kreutzer
","Christophe, C., Philippe, A., Guérin, G., Kreutzer, S., 2024. SCMatrix(): Construct the Stratigraphic Constrain Matrix Interactively. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+"SCMatrix","Construct the Stratigraphic Constrain Matrix Interactively","This function helps to define the stratigraphic relation between samples using questions. The output of this function can be used in the function AgeS_Computation .",NA,NA,NA,"Claire Christophe, Anne Philippe, Guillaume Guérin, Sebastian Kreutzer
","Christophe, C., Philippe, A., Guérin, G., Kreutzer, S., 2024. SCMatrix(): Construct the Stratigraphic Constrain Matrix Interactively. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"SHCal13","
Atmospheric South data for calibration of 14C age ","As 14C years is not equal to calendar years because atmospheric 14C concentration varies through time. Hence, data in AtmosphericSouth_CalC14 allows a calibration for mid-latitude Southern Hemisphere atmospher reservoir.",NA,NA,NA,NA,NA
"SHCal20","
Atmospheric South data for calibration of 14C age ","As 14C years is not equal to calendar years because atmospheric 14C concentration varies through time. Hence, data in AtmosphericSouth_CalC14 allows a calibration for mid-latitude Southern Hemisphere atmospher reservoir.",NA,NA,NA,NA,NA
"write_BayLumFiles","Write BayLum .csv-files","This function allows the user to write all .csv files expected by Generate_DataFile and Generate_DataFile_MG . Unlike create_FolderTemplates , this function makes it possible to write .csv files with all information directly from R. No further modification of .csv files are required. The purpose of this function is (i) to reduce tedious manual editing of .csv-files and the errors that result (ii) to introduce an easy way to review information inside .csv-files (by revisiting code rather than opening individual .csv-files) and (iii) to streamline folder and file creation when preparing data to run BayLum's modelling functions. Note: the user will still need to move the appropriate .bin-files into all the sample folders.","0.1.0
-",NA,NA,"Frederik Baumgarten, RadPhys, DTU Physics, Technical University of Denmark (Denmark)
","Baumgarten, F.H., 2024. write_BayLumFiles(): Write BayLum .csv-files. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+",NA,NA,"Frederik Baumgarten, RadPhys, DTU Physics, Technical University of Denmark (Denmark)
","Baumgarten, F.H., 2024. write_BayLumFiles(): Write BayLum .csv-files. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
"write_YAMLConfigFile","Write Auto Generated YAML BayLum Configuration File to the Disc","This little function helps to auto-generate a the BayLum YAML configuration file or a list that can be passed to create_DataFile . The YAML file itself can be modified in any text editor. The allowed parameters are extracted from the reference YAML file","0.1.0
-",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl University of Heidelberg (Germany)
","Kreutzer, S., 2024. write_YAMLConfigFile(): Write Auto Generated YAML BayLum Configuration File to the Disc. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-59. https://CRAN.r-project.org/package=BayLum
+",NA,NA,"Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl University of Heidelberg (Germany)
","Kreutzer, S., 2024. write_YAMLConfigFile(): Write Auto Generated YAML BayLum Configuration File to the Disc. Function version 0.1.0. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2024. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.2.9000-61. https://CRAN.r-project.org/package=BayLum
"
diff --git a/BayLum.BuildResults/BayLum_0.3.2.9000-59-Functions.html b/BayLum.BuildResults/BayLum_0.3.2.9000-61-Functions.html
similarity index 96%
rename from BayLum.BuildResults/BayLum_0.3.2.9000-59-Functions.html
rename to BayLum.BuildResults/BayLum_0.3.2.9000-61-Functions.html
index fba2668e..492d6fea 100644
--- a/BayLum.BuildResults/BayLum_0.3.2.9000-59-Functions.html
+++ b/BayLum.BuildResults/BayLum_0.3.2.9000-61-Functions.html
@@ -1,6 +1,6 @@
Major functions in the R package 'Luminescence'
- [version: 0.3.2.9000-59 ]
+ [version: 0.3.2.9000-61 ]