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tesselle · Feb 26, 2024 · 5116f8a · 5116f8a
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diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ message: 'To cite package "nexus" in publications use:'
 type: software
 license: GPL-3.0-or-later
 title: 'nexus: Sourcing Archaeological Materials by Chemical Composition'
-version: 0.1.0
+version: 0.2.0
 doi: 10.5281/zenodo.10225630
 abstract: 'Exploration and analysis of compositional data in the framework of Aitchison
   (1986, ISBN: 978-94-010-8324-9). This package provides tools for chemical fingerprinting
@@ -38,10 +38,10 @@ preferred-citation:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-5331-5087
     affiliation: Université de Nantes
-  year: '2023'
+  year: '2024'
   location:
     name: Pessac, France
-  notes: R package version 0.1.0
+  notes: R package version 0.2.0
   url: https://packages.tesselle.org/nexus/
   doi: 10.5281/zenodo.10225630
   institution:
@@ -71,38 +71,38 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
   version: '>= 3.5'
 - type: software
-  title: arkhe
-  abstract: 'arkhe: Tools for Cleaning Rectangular Data'
-  notes: Imports
-  url: https://packages.tesselle.org/arkhe/
-  repository: https://CRAN.R-project.org/package=arkhe
+  title: dimensio
+  abstract: 'dimensio: Multivariate Data Analysis'
+  notes: Depends
+  url: https://packages.tesselle.org/dimensio/
+  repository: https://CRAN.R-project.org/package=dimensio
   authors:
   - family-names: Frerebeau
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  year: '2023'
-  version: '>= 1.4.0'
+  year: '2024'
+  version: '>= 0.6.0'
 - type: software
-  title: dimensio
-  abstract: 'dimensio: Multivariate Data Analysis'
+  title: arkhe
+  abstract: 'arkhe: Tools for Cleaning Rectangular Data'
   notes: Imports
-  url: https://packages.tesselle.org/dimensio/
-  repository: https://CRAN.R-project.org/package=dimensio
+  url: https://packages.tesselle.org/arkhe/
+  repository: https://CRAN.R-project.org/package=arkhe
   authors:
   - family-names: Frerebeau
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  year: '2023'
-  version: '>= 0.5.0'
+  year: '2024'
+  version: '>= 1.6.0'
 - type: software
   title: graphics
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -111,7 +111,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -122,7 +122,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -137,8 +137,8 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  year: '2023'
-  version: '>= 1.0.0'
+  year: '2024'
+  version: '>= 1.2.0'
 - type: software
   title: methods
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -147,7 +147,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -160,7 +160,7 @@ references:
   - family-names: Ripley
     given-names: Brian
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: stats
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -169,7 +169,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -180,7 +180,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -205,7 +205,7 @@ references:
     given-names: Mia
     email: [email protected]
     orcid: https://orcid.org/0000-0001-6398-4850
-  year: '2023'
+  year: '2024'
 - type: software
   title: folio
   abstract: 'folio: Datasets for Teaching Archaeology and Paleontology'
@@ -218,7 +218,8 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  year: '2023'
+  year: '2024'
+  version: '>= 1.4.0'
 - type: software
   title: igraph
   abstract: 'igraph: Network Analysis and Visualization'
@@ -251,7 +252,7 @@ references:
     given-names: Kirill
     email: [email protected]
     orcid: https://orcid.org/0000-0002-1416-3412
-  year: '2023'
+  year: '2024'
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -263,50 +264,23 @@ references:
     given-names: Yihui
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
-  year: '2023'
+  year: '2024'
 - type: software
-  title: rmarkdown
-  abstract: 'rmarkdown: Dynamic Documents for R'
+  title: markdown
+  abstract: 'markdown: Render Markdown with ''commonmark'''
   notes: Suggests
-  url: https://pkgs.rstudio.com/rmarkdown/
-  repository: https://CRAN.R-project.org/package=rmarkdown
+  url: https://github.com/rstudio/markdown
+  repository: https://CRAN.R-project.org/package=markdown
   authors:
-  - family-names: Allaire
-    given-names: JJ
-    email: [email protected]
   - family-names: Xie
     given-names: Yihui
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
-  - family-names: Dervieux
-    given-names: Christophe
-    email: [email protected]
-    orcid: https://orcid.org/0000-0003-4474-2498
-  - family-names: McPherson
-    given-names: Jonathan
-    email: [email protected]
-  - family-names: Luraschi
-    given-names: Javier
-  - family-names: Ushey
-    given-names: Kevin
-    email: [email protected]
-  - family-names: Atkins
-    given-names: Aron
-    email: [email protected]
-  - family-names: Wickham
-    given-names: Hadley
-    email: [email protected]
-  - family-names: Cheng
-    given-names: Joe
-    email: [email protected]
-  - family-names: Chang
-    given-names: Winston
-    email: [email protected]
-  - family-names: Iannone
-    given-names: Richard
-    email: [email protected]
-    orcid: https://orcid.org/0000-0003-3925-190X
-  year: '2023'
+  - family-names: Allaire
+    given-names: JJ
+  - family-names: Horner
+    given-names: Jeffrey
+  year: '2024'
 - type: software
   title: rsvg
   abstract: 'rsvg: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or
@@ -319,7 +293,7 @@ references:
     given-names: Jeroen
     email: [email protected]
     orcid: https://orcid.org/0000-0002-4035-0289
-  year: '2023'
+  year: '2024'
 - type: software
   title: svglite
   abstract: 'svglite: An ''SVG'' Graphics Device'
@@ -346,7 +320,7 @@ references:
   - family-names: Lise
     given-names: Vaudor
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: tinysnapshot
   abstract: 'tinysnapshot: Snapshots for Unit Tests using the ''tinytest'' Framework'
@@ -358,7 +332,7 @@ references:
     given-names: Vincent
     email: [email protected]
     orcid: https://orcid.org/0000-0003-2042-7063
-  year: '2023'
+  year: '2024'
 - type: software
   title: tinytest
   abstract: 'tinytest: Lightweight and Feature Complete Unit Testing Framework'
@@ -370,7 +344,7 @@ references:
     given-names: Mark
     email: [email protected]
     orcid: https://orcid.org/0000-0002-9807-4686
-  year: '2023'
+  year: '2024'
 identifiers:
 - description: The concept DOI.
   type: doi

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: nexus
 Title: Sourcing Archaeological Materials by Chemical Composition
-Version: 0.1.0.9000
+Version: 0.2.0
 Authors@R: c(
     person("Nicolas", "Frerebeau", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5759-4944", affiliation = "Université Bordeaux Montaigne")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# nexus 0.1.0.9000
+# nexus 0.2.0
 ## New classes and methods
 * Add `hist()` methods to plot ILR histograms.
 * Add `quantile()` methods for compositional data matrix.

diff --git a/R/nexus-package.R b/R/nexus-package.R
@@ -2,9 +2,9 @@
 #'  \tabular{ll}{
 #'   **Package:** \tab nexus \cr
 #'   **Type:** \tab Package \cr
-#'   **Version:** \tab 0.1.0 \cr
+#'   **Version:** \tab 0.2.0 \cr
 #'   **License:** \tab GPL-3 \cr
-#'   **Zenodo:** \tab  \cr
+#'   **Zenodo:** \tab \doi{10.5281/zenodo.10225630} \cr
 #'  }
 #'
 #' @section Package options:

diff --git a/README.Rmd b/README.Rmd
@@ -94,7 +94,7 @@ head(coda)
 
 **nexus** allows to specify whether an observation belongs to a specific group (or not). Additionally, the presence of repeated measurements can be specified by giving several observations the same sample name:
 
-```{r groups}
+```{r groups, fig.width=7, fig.height=5, fig.align='center'}
 ## Mineral compositions of five slides as reported by five analysts
 ## Data from Aitchison 1986
 data("slides")
@@ -103,6 +103,9 @@ head(slides)
 ## Coerce to compositional data
 coda <- as_composition(slides, sample = 2, group = 1)
 head(coda)
+
+## Grouped compositional barplots
+barplot(coda, order = 1)
 ```
 
 ## Contributing

diff --git a/README.md b/README.md
@@ -57,21 +57,21 @@ companion package to **nexus** that allows to create ternary plots.
 
     To cite nexus in publications use:
 
-      Frerebeau N, Philippe A (2023). _nexus: Sourcing Archaeological
+      Frerebeau N, Philippe A (2024). _nexus: Sourcing Archaeological
       Materials by Chemical Composition_. Université Bordeaux Montaigne,
       Pessac, France. doi:10.5281/zenodo.10225630
-      <https://doi.org/10.5281/zenodo.10225630>, R package version 0.1.0,
+      <https://doi.org/10.5281/zenodo.10225630>, R package version 0.2.0,
       <https://packages.tesselle.org/nexus/>.
 
     A BibTeX entry for LaTeX users is
 
       @Manual{,
         author = {Nicolas Frerebeau and Anne Philippe},
         title = {{nexus: Sourcing Archaeological Materials by Chemical Composition}},
-        year = {2023},
+        year = {2024},
         organization = {Université Bordeaux Montaigne},
         address = {Pessac, France},
-        note = {R package version 0.1.0},
+        note = {R package version 0.2.0},
         url = {https://packages.tesselle.org/nexus/},
         doi = {10.5281/zenodo.10225630},
       }
@@ -100,6 +100,7 @@ remotes::install_github("tesselle/nexus")
 ``` r
 ## Load the package
 library(nexus)
+#> Loading required package: dimensio
 ```
 
 **nexus** provides a set of S4 classes that represent different special
@@ -183,8 +184,13 @@ head(coda)
 #> 4 0.005000000
 #> 5 0.003000000
 #> 6 0.003000000
+
+## Grouped compositional barplots
+barplot(coda, order = 1)
 ```
 
+<img src="man/figures/README-groups-1.png" style="display: block; margin: auto;" />
+
 ## Contributing
 
 Please note that the **nexus** project is released with a [Contributor