Update funding details and add logos

Author: nfrerebeau

DESCRIPTION

@@ -1,48 +1,66 @@
-Package: BayLum
 Type: Package
+Package: BayLum
 Title: Chronological Bayesian Models Integrating Optically Stimulated
-        Luminescence and Radiocarbon Age Dating
-Description: Bayesian analysis of luminescence data and C-14 age estimates. Bayesian models are based on the following publications: Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003> and Combes et al. (2015) <doi:10.1016/j.quageo.2015.04.001>. This includes, amongst others, data import, export, application of age models and palaeodose model.
-Date: 2024-07-12
+    Luminescence and Radiocarbon Age Dating
 Version: 0.3.3.9000-13
-Author: Claire Christophe [aut], 
-    Anne Philippe [aut, cre] (<https://orcid.org/0000-0002-5331-5087>), 
-    Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>), 
-    Guillaume Guérin [aut] (<https://orcid.org/0000-0001-6298-5579>),
-    Frederik Harly Baumgarten [aut] (<https://orcid.org/0000-0002-4374-5948>),
-    Nicolas Frerebeau [aut] (<https://orcid.org/0000-0001-5759-4944>)
+Date: 2024-07-12
 Authors@R: c(
-    person("Claire", "Christophe", role = c("aut")),
-    person("Anne", "Philippe", role = c("aut", "cre"), email = "[email protected]",  comment = c(ORCID = "0000-0002-5331-5087")),
-    person("Sebastian", "Kreutzer", role = "aut", comment = c(ORCID = "0000-0002-0734-2199")),
-    person("Guillaume", "Guérin", role = "aut", comment = c(ORCID = "0000-0001-6298-5579")),
-    person("Frederik Harly", "Baumgarten", role = "aut", comment = c(ORCID = "0000-0002-4374-5948")),
-    person("Nicolas", "Frerebeau", role = "aut", comment = c(ORCID = "0000-0001-5759-4944")))
+    person("Claire", "Christophe", role = "aut"),
+    person("Anne", "Philippe", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-5331-5087")),
+    person("Sebastian", "Kreutzer", role = "aut",
+           comment = c(ORCID = "0000-0002-0734-2199")),
+    person("Guillaume", "Guérin", role = "aut",
+           comment = c(ORCID = "0000-0001-6298-5579")),
+    person("Frederik Harly", "Baumgarten", role = "aut",
+           comment = c(ORCID = "0000-0002-4374-5948")),
+    person("Nicolas", "Frerebeau", role = "aut",
+           comment = c(ORCID = "0000-0001-5759-4944")),
+    person("Université Bordeaux Montaigne", role = c("cph", "fnd")),
+    person("CNRS", role = "fnd"),
+    person("LabEx Sciences archéologiques de Bordeaux", role = "fnd")
+  )
+Author: Claire Christophe [aut], Anne Philippe [aut, cre]
+    (<https://orcid.org/0000-0002-5331-5087>), Sebastian Kreutzer [aut]
+    (<https://orcid.org/0000-0002-0734-2199>), Guillaume Guérin [aut]
+    (<https://orcid.org/0000-0001-6298-5579>), Frederik Harly Baumgarten
+    [aut] (<https://orcid.org/0000-0002-4374-5948>), Nicolas Frerebeau
+    [aut] (<https://orcid.org/0000-0001-5759-4944>) Université Bordeaux
+    Montaigne [cph, fnd] CNRS [fnd] LabEx Sciences archéologiques de
+    Bordeaux [fnd]
 Maintainer: Anne Philippe <[email protected]>
+Description: Bayesian analysis of luminescence data and C-14 age
+    estimates. Bayesian models are based on the following publications:
+    Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003>
+    and Combes et al. (2015) <doi:10.1016/j.quageo.2015.04.001>. This
+    includes, amongst others, data import, export, application of age
+    models and palaeodose model.
+License: GPL-3
+URL: https://CRAN.r-project.org/package=BayLum,
+    https://crp2a.github.io/BayLum/
+BugReports: https://github.com/crp2a/BayLum/issues
 Depends: 
-  R (>= 4.3), 
-  utils, 
-  coda (>= 0.19)
+    coda (>= 0.19),
+    R (>= 4.3),
+    utils
 Imports: 
-  methods, 
-  hexbin (>= 1.28.3), 
-  cli (>= 3.6.1),
-  KernSmooth (>= 2.23), 
-  rjags (>= 4-15), 
-  runjags (>= 2.2.2), 
-  Luminescence (>= 0.9.24),
-  yaml (>= 2.3.9)
+    cli (>= 3.6.1),
+    hexbin (>= 1.28.3),
+    KernSmooth (>= 2.23),
+    Luminescence (>= 0.9.24),
+    methods,
+    rjags (>= 4-15),
+    runjags (>= 2.2.2),
+    yaml (>= 2.3.9)
 Suggests: 
-    testthat (>= 3.2.1),
     knitr,
-    rmarkdown
-License: GPL-3
-Language: en-GB
+    rmarkdown,
+    testthat (>= 3.2.1)
+VignetteBuilder: 
+    knitr
 Encoding: UTF-8
-URL: https://CRAN.r-project.org/package=BayLum, https://crp2a.github.io/BayLum/
-BugReports: https://github.com/crp2a/BayLum/issues
+Language: en-GB
 LazyData: true
 NeedsCompilation: no
-SystemRequirements: JAGS >= 4.3.2 (https://mcmc-jags.sourceforge.io/)
-VignetteBuilder: knitr
 RoxygenNote: 7.3.2
+SystemRequirements: JAGS >= 4.3.2 (https://mcmc-jags.sourceforge.io/)

R/BayLum-package.R

@@ -1,36 +1,42 @@
-#' @title Chronological Bayesian Models Integrating Optically Stimulated Luminescence and C-14 Dating\cr
-#'
-#' \if{html}{
-#' \figure{BayLum_logo.png}{options: width="50"}\cr
-#' }
-#'
-#' @description A collection of various R functions for Bayesian analysis of luminescence
-#' data and C-14 age estimates. This includes, amongst others, data import, export,
-#' application of age and palaeodose models.
-#'
+#' @title
+#'  Chronological Bayesian Models Integrating Optically Stimulated Luminescence
+#'  and C-14 Dating
+#' @description
+#'  A collection of various R functions for Bayesian analysis of luminescence
+#'  data and C-14 age estimates. This includes, amongst others, data import,
+#'  export, application of age and palaeodose models.
+#' @details
+#'  This package is based on the functions: [Generate_DataFile()] and
+#'  [Generate_DataFile_MG()] to import luminescence data. These functions create
+#'  a list containing all informations to compute age of single-grain OSL
+#'  measurements for the first function and multi-grain OSL measurements for
+#'  the second.
+#'
+#'  The functions: [Age_Computation()] and [AgeS_Computation()] use Bayesian
+#'  analysis for OSL age estimation for one or various samples according to
+#'  difference models (e.g. different dose-response curves and different
+#'  equivalent dose distributions around the palaeodose).
+#'
+#'  It is possible to consider various BIN/BINX-files per sample, to compute
+#'  ages of samples in stratigraphic constraints and to integrate systematic
+#'  errors.
+#'
+#'  It is possible to calibrate C-14 age with the function
+#'  [AgeC14_Computation()]. We can also estimate chronology containing 14C age
+#'  and OSL samples with the function [Age_OSLC14()].
+#' @references
+#'  Philippe, A., Guérin, G., Kreutzer, S., 2019. BayLum - An R package for
+#'  Bayesian analysis of OSL ages: An introduction. *Quaternary Geochronology*
+#'  49, 16-24. \doi{10.1016/j.quageo.2018.05.009}
+#' @note
+#'  This work received a state financial support managed by the Agence Nationale
+#'  de la Recherche (France) through the program *Investissements d'avenir*
+#'  (ref. [ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr).
 #' @name BayLum-package
 #' @aliases BayLum-package BayLum
-#' @keywords package
-#' @details This package is based on the functions: [Generate_DataFile] and [Generate_DataFile_MG]
-#' to import luminescence data. These functions create a list containing all informations to
-#' compute age of single-grain OSL measurements for the first function and multi-grain OSL
-#' measurements for the second.
-#'
-#' The functions: [Age_Computation] and [AgeS_Computation] use Bayesian analysis for OSL age
-#' estimation for one or various samples according to difference models
-#' (e.g. different dose-response curves and different equivalent dose distributions around the palaeodose).
-#'
-#' It is possible to consider various BIN/BINX-files per sample, to compute ages of samples in
-#' stratigraphic constraints and to integrate systematic errors.
-#'
-#' It is possible to calibrate C-14 age with the function [AgeC14_Computation].
-#' We can also estimate chronology containing 14C age and OSL samples with the function [Age_OSLC14].
-#'
-#' @references
-#'
-#' Philippe, A., Guérin, G., Kreutzer, S., 2019. BayLum - An R package for Bayesian analysis of OSL ages:
-#' An introduction. Quaternary Geochronology 49, 16–24. \doi{10.1016/j.quageo.2018.05.009}
-#'
-#' @md
-#' @import utils stats methods graphics grDevices coda
+#' @docType package
+#' @keywords internal
 "_PACKAGE"
+
+#' @import utils stats methods graphics grDevices coda
+NULL

README.Rmd

@@ -15,10 +15,10 @@ knitr::opts_chunk$set(
 library(BayLum)
 ```
 
-# BayLum <img width=120px src="man/figures/BayLum_logo.png" align="right" />
+# BayLum <img width=120px src="man/figures/logo_BayLum.png" align="right" />
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/crp2a/BayLum/workflows/GitHub Actions CI/badge.svg)](https://github.com/crp2a/BayLum/actions)
+[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml)
 [![codecov](https://codecov.io/gh/crp2a/BayLum/graph/badge.svg?token=cOdZr6imKX)](https://app.codecov.io/gh/crp2a/BayLum)
 
 [![r-universe](https://crp2a.r-universe.dev/badges/BayLum)](https://crp2a.r-universe.dev/BayLum)
@@ -63,8 +63,7 @@ the package on [CRAN 'BayLum'](https://CRAN.R-project.org/package=BayLum ).
 
 ## Funding
 
-The development of `'BayLum'`  was supported by LabEx LaScArBx (ANR -n.ANR-10-LABX-52) between
-2015 and 2018 (in particular through the MAM and COVADIM projects).
+The development of `'BayLum'` received a state financial support managed by the Agence Nationale de la Recherche (France) through the program *Investissements d'avenir* (ref. [ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and 2018.
 
 ## License
 

README.md

@@ -5,11 +5,11 @@
 
 <!-- README.md was auto-generated by README.Rmd. Please DO NOT edit by hand!-->
 
-# BayLum <img width=120px src="man/figures/BayLum_logo.png" align="right" />
+# BayLum <img width=120px src="man/figures/logo_BayLum.png" align="right" />
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/crp2a/BayLum/workflows/GitHub%20Actions%20CI/badge.svg)](https://github.com/crp2a/BayLum/actions)
+[![R-CMD-check](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml/badge.svg)](https://github.com/crp2a/BayLum/actions/workflows/GitHub_Actions_CI.yaml)
 [![codecov](https://codecov.io/gh/crp2a/BayLum/graph/badge.svg?token=cOdZr6imKX)](https://app.codecov.io/gh/crp2a/BayLum)
 
 [![r-universe](https://crp2a.r-universe.dev/badges/BayLum)](https://crp2a.r-universe.dev/BayLum)
@@ -73,9 +73,11 @@ change day by day. For stable branches please visit the package on [CRAN
 
 ## Funding
 
-The development of `'BayLum'` was supported by LabEx LaScArBx (ANR
--n.ANR-10-LABX-52) between 2015 and 2018 (in particular through the MAM
-and COVADIM projects).
+The development of `'BayLum'` received a state financial support managed
+by the Agence Nationale de la Recherche (France) through the program
+*Investissements d’avenir* (ref.
+[ANR-10-LABX-52](https://lascarbx.labex.u-bordeaux.fr)) between 2015 and
+2018.
 
 ## License
 

_pkgdown.yml

@@ -2,6 +2,20 @@ url: https://crp2a.github.io/BayLum/
 development:
   mode: auto
 
+authors:
+  Archéosciences Bordeaux:
+    href: https://www.archeosciences-bordeaux.fr.fr
+    html: <img src="https://crp2a.github.io/BayLum/reference/figures/logo_archeosciences.jpg" />
+  Université Bordeaux Montaigne:
+    href: https://www.u-bordeaux-montaigne.fr
+    html: <img src="https://crp2a.github.io/BayLum/reference/figures/logo_ubm.jpg" />
+  CNRS:
+    href: https://www.cnrs.fr
+    html: <img src="https://crp2a.github.io/BayLum/reference/figures/logo_cnrs.jpg" />
+  LabEx Sciences archéologiques de Bordeaux:
+    href: https://lascarbx.labex.u-bordeaux.fr
+    html: <img src="https://crp2a.github.io/BayLum/reference/figures/logo_idex.png" />
+
 navbar:
   title: BayLum
   left: