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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: 0.3.0
+version: 0.4.0
 doi: 10.5281/zenodo.10225630
 identifiers:
 - description: The concept DOI.
@@ -23,6 +23,9 @@ identifiers:
 - description: The versioned DOI for version 0.3.0.
   type: doi
   value: 10.5281/zenodo.13646482
+- description: The CRAN DOI
+  type: doi
+  value: 10.32614/cran.package.nexus
 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
   and source tracking of ancient materials.'
@@ -31,12 +34,10 @@ authors:
   given-names: Nicolas
   email: [email protected]
   orcid: https://orcid.org/0000-0001-5759-4944
-  affiliation: Université Bordeaux Montaigne
 - family-names: Philippe
   given-names: Anne
   email: [email protected]
   orcid: https://orcid.org/0000-0002-5331-5087
-  affiliation: Université de Nantes
 preferred-citation:
   type: manual
   title: 'nexus: Sourcing Archaeological Materials by Chemical Composition'
@@ -45,17 +46,15 @@ preferred-citation:
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
-    affiliation: Université Bordeaux Montaigne
   - family-names: Philippe
     given-names: Anne
     email: [email protected]
     orcid: https://orcid.org/0000-0002-5331-5087
-    affiliation: Université de Nantes
-  year: '2024'
+  year: '2025'
   institution:
     name: Université Bordeaux Montaigne
     address: Pessac, France
-  notes: R package version 0.3.0
+  notes: R package version 0.4.0
   url: https://packages.tesselle.org/nexus/
   doi: 10.5281/zenodo.10225630
 repository: https://CRAN.R-project.org/package=nexus
@@ -66,7 +65,6 @@ contact:
   given-names: Nicolas
   email: [email protected]
   orcid: https://orcid.org/0000-0001-5759-4944
-  affiliation: Université Bordeaux Montaigne
 keywords:
 - archaeology
 - archaeological science
@@ -84,7 +82,7 @@ references:
   institution:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
-  year: '2024'
+  year: '2025'
   version: '>= 3.5'
 - type: software
   title: dimensio
@@ -97,10 +95,9 @@ references:
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
-    affiliation: Université Bordeaux Montaigne
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.dimensio
-  version: '>= 0.9.0'
+  version: '>= 0.11.0'
 - type: software
   title: arkhe
   abstract: 'arkhe: Tools for Cleaning Rectangular Data'
@@ -112,10 +109,9 @@ references:
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
-    affiliation: Université Bordeaux Montaigne
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.arkhe
-  version: '>= 1.7.0'
+  version: '>= 1.9.0'
 - type: software
   title: graphics
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -125,7 +121,7 @@ references:
   institution:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
-  year: '2024'
+  year: '2025'
 - type: software
   title: grDevices
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -135,7 +131,7 @@ references:
   institution:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
-  year: '2024'
+  year: '2025'
 - type: software
   title: isopleuros
   abstract: 'isopleuros: Ternary Plots'
@@ -147,10 +143,9 @@ references:
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
-    affiliation: Université Bordeaux Montaigne
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.isopleuros
-  version: '>= 1.2.0'
+  version: '>= 1.3.0'
 - type: software
   title: khroma
   abstract: 'khroma: Colour Schemes for Scientific Data Visualization'
@@ -162,10 +157,9 @@ references:
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
-    affiliation: Université Bordeaux Montaigne
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.khroma
-  version: '>= 1.14.0'
+  version: '>= 1.15.0'
 - type: software
   title: methods
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -175,7 +169,7 @@ references:
   institution:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
-  year: '2024'
+  year: '2025'
 - type: software
   title: MASS
   abstract: 'MASS: Support Functions and Datasets for Venables and Ripley''s MASS'
@@ -188,7 +182,7 @@ references:
     email: [email protected]
   - family-names: Venables
     given-names: Bill
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.MASS
 - type: software
   title: stats
@@ -199,7 +193,7 @@ references:
   institution:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
-  year: '2024'
+  year: '2025'
 - type: software
   title: utils
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -209,7 +203,7 @@ references:
   institution:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
-  year: '2024'
+  year: '2025'
 - type: software
   title: cluster
   abstract: 'cluster: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw
@@ -232,7 +226,7 @@ references:
     given-names: Mia
     email: [email protected]
     orcid: https://orcid.org/0000-0001-6398-4850
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.cluster
 - type: software
   title: folio
@@ -246,7 +240,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.folio
   version: '>= 1.5.0'
 - type: software
@@ -281,7 +275,7 @@ references:
     given-names: Kirill
     email: [email protected]
     orcid: https://orcid.org/0000-0002-1416-3412
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.igraph
 - type: software
   title: knitr
@@ -294,7 +288,7 @@ references:
     given-names: Yihui
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.knitr
 - type: software
   title: markdown
@@ -311,7 +305,7 @@ references:
     given-names: JJ
   - family-names: Horner
     given-names: Jeffrey
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.markdown
 - type: software
   title: rsvg
@@ -323,9 +317,9 @@ references:
   authors:
   - family-names: Ooms
     given-names: Jeroen
-    email: [email protected]
+    email: [email protected]
     orcid: https://orcid.org/0000-0002-4035-0289
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.rsvg
 - type: software
   title: svglite
@@ -353,7 +347,7 @@ references:
   - family-names: Lise
     given-names: Vaudor
     email: [email protected]
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.svglite
 - type: software
   title: tinysnapshot
@@ -366,7 +360,7 @@ references:
     given-names: Vincent
     email: [email protected]
     orcid: https://orcid.org/0000-0003-2042-7063
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.tinysnapshot
 - type: software
   title: tinytest
@@ -380,6 +374,6 @@ references:
     name-particle: van der
     email: [email protected]
     orcid: https://orcid.org/0000-0002-9807-4686
-  year: '2024'
+  year: '2025'
   doi: 10.32614/CRAN.package.tinytest
 

DESCRIPTION

@@ -1,15 +1,13 @@
 Package: nexus
 Title: Sourcing Archaeological Materials by Chemical Composition
-Version: 0.3.0.9000
+Version: 0.4.0
 Authors@R: c(
     person("Nicolas", "Frerebeau", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-5759-4944", affiliation = "Université Bordeaux Montaigne")),
+           comment = c(ORCID = "0000-0001-5759-4944")),
     person("Anne", "Philippe", , "[email protected]", role = "aut",
-           comment = c(ORCID = "0000-0002-5331-5087", affiliation = "Université de Nantes")),
+           comment = c(ORCID = "0000-0002-5331-5087")),
     person("Brice", "Lebrun", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0001-7503-8685", "Logo designer")),
-    person("Arthur", "Leck", , "[email protected]", role = "ctb",
-           comment = c(ORCID = "0009-0004-8819-9970", affiliation = "Université Bordeaux Montaigne")),
     person("Université Bordeaux Montaigne", role = "fnd"),
     person("CNRS", role = "fnd")
   )

NEWS.md

@@ -1,8 +1,9 @@
-# nexus 0.3.0.9000
+# nexus 0.4.0
 ## New classes and methods
 * Add `ReferenceGroups`, `GroupedComposition` and `GroupedLogRatio` classes to represent grouped data.
 * Add `group()`, `ungroup()`, `group_levels()`, `group_names()`, `group_indices()`, `group_rows()`, `group_length()`, `group_size()`, `group_extract()`, `group_split()` and `is_grouped()` to work with grouped data.
 * Add `transform_lr()`, `transform_clr()`, `transform_alr()`, `transform_ilr()`, `transform_plr()` and `transform_inverse()` methods for `GroupedComposition` and `GroupedLogRatio` objects.
+* Add `is_composition()`, `is_logratio()` and `is_grouped()` to check if an object is from a specific class.
 * Add `pairs()` to display a matrix of ternary plots.
 
 ## Enhancements

R/nexus-package.R

@@ -2,7 +2,7 @@
 #'  \tabular{ll}{
 #'   **Package:** \tab nexus \cr
 #'   **Type:** \tab Package \cr
-#'   **Version:** \tab 0.3.0 \cr
+#'   **Version:** \tab 0.4.0 \cr
 #'   **License:** \tab GPL-3 \cr
 #'   **Zenodo:** \tab \doi{10.5281/zenodo.10225630} \cr
 #'  }

README.Rmd

@@ -13,7 +13,7 @@ knitr::opts_chunk$set(
   fig.path = "man/figures/README-",
   out.width = NULL
 )
-Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
+Sys.setenv(LANGUAGE = "en") # Force locale
 ```
 
 # nexus <img width=120px src="man/figures/logo.png" align="right" />
@@ -115,8 +115,12 @@ clr <- transform_clr(coda, weights = TRUE)
 lra <- pca(clr)
 
 ## Visualize results
-viz_individuals(lra, color = c("#004488", "#DDAA33", "#BB5566"))
-viz_hull(x = lra, color = c("#004488", "#DDAA33", "#BB5566"))
+viz_individuals(
+  x = lra, 
+  extra_quali = group_names(clr),
+  color = c("#004488", "#DDAA33", "#BB5566"),
+  hull = TRUE
+)
 
 viz_variables(lra)
 ```

README.md

@@ -65,10 +65,10 @@ companion package to **nexus** that allows to create ternary plots.
 
 To cite nexus in publications use:
 
-Frerebeau N, Philippe A (2024). *nexus: Sourcing Archaeological
+Frerebeau N, Philippe A (2025). *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 0.3.0.9000,
+<https://doi.org/10.5281/zenodo.10225630>, R package version 0.4.0,
 <https://packages.tesselle.org/nexus/>.
 
 This package is a part of the tesselle project
@@ -139,8 +139,12 @@ clr <- transform_clr(coda, weights = TRUE)
 lra <- pca(clr)
 
 ## Visualize results
-viz_individuals(lra, color = c("#004488", "#DDAA33", "#BB5566"))
-viz_hull(x = lra, color = c("#004488", "#DDAA33", "#BB5566"))
+viz_individuals(
+  x = lra, 
+  extra_quali = group_names(clr),
+  color = c("#004488", "#DDAA33", "#BB5566"),
+  hull = TRUE
+)
 
 viz_variables(lra)
 ```
@@ -329,6 +333,15 @@ Taylor & Francis Group.
 
 </div>
 
+<div id="ref-greenacre2024" class="csl-entry">
+
+Greenacre, Michael, and Jonathan R. Wood. 2024. “A Comprehensive
+Workflow for Compositional Data Analysis in Archaeometry, with Code in
+R.” *Archaeological and Anthropological Sciences* 16 (10): 171.
+<https://doi.org/10.1007/s12520-024-02070-w>.
+
+</div>
+
 <div id="ref-grunsky2024" class="csl-entry">
 
 Grunsky, Eric, Michael Greenacre, and Bruce Kjarsgaard. 2024. “GeoCoDA: