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tesselle · Sep 3, 2024 · 1afb113 · 1afb113
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diff --git a/CITATION.cff b/CITATION.cff
@@ -10,6 +10,16 @@ license: GPL-3.0-or-later
 title: 'nexus: Sourcing Archaeological Materials by Chemical Composition'
 version: 0.3.0
 doi: 10.5281/zenodo.10225630
+identifiers:
+- description: The concept DOI.
+  type: doi
+  value: 10.5281/zenodo.10225630
+- description: The versioned DOI for version 0.1.0.
+  type: doi
+  value: 10.5281/zenodo.10225631
+- description: The versioned DOI for version 0.2.0.
+  type: doi
+  value: 10.5281/zenodo.10711236
 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.'
@@ -86,7 +96,8 @@ references:
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
   year: '2024'
-  version: '>= 0.8.0'
+  doi: 10.32614/CRAN.package.dimensio
+  version: '>= 0.9.0'
 - type: software
   title: arkhe
   abstract: 'arkhe: Tools for Cleaning Rectangular Data'
@@ -100,7 +111,8 @@ references:
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
   year: '2024'
-  version: '>= 1.6.0'
+  doi: 10.32614/CRAN.package.arkhe
+  version: '>= 1.7.0'
 - type: software
   title: graphics
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -134,7 +146,23 @@ references:
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
   year: '2024'
+  doi: 10.32614/CRAN.package.isopleuros
   version: '>= 1.2.0'
+- type: software
+  title: khroma
+  abstract: 'khroma: Colour Schemes for Scientific Data Visualization'
+  notes: Imports
+  url: https://packages.tesselle.org/khroma/
+  repository: https://CRAN.R-project.org/package=khroma
+  authors:
+  - family-names: Frerebeau
+    given-names: Nicolas
+    email: [email protected]
+    orcid: https://orcid.org/0000-0001-5759-4944
+    affiliation: Université Bordeaux Montaigne
+  year: '2024'
+  doi: 10.32614/CRAN.package.khroma
+  version: '>= 1.14.0'
 - type: software
   title: methods
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -155,7 +183,10 @@ references:
   - family-names: Ripley
     given-names: Brian
     email: [email protected]
+  - family-names: Venables
+    given-names: Bill
   year: '2024'
+  doi: 10.32614/CRAN.package.MASS
 - type: software
   title: stats
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -199,6 +230,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-6398-4850
   year: '2024'
+  doi: 10.32614/CRAN.package.cluster
 - type: software
   title: folio
   abstract: 'folio: Datasets for Teaching Archaeology and Paleontology'
@@ -212,7 +244,8 @@ references:
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
   year: '2024'
-  version: '>= 1.4.0'
+  doi: 10.32614/CRAN.package.folio
+  version: '>= 1.5.0'
 - type: software
   title: igraph
   abstract: 'igraph: Network Analysis and Visualization'
@@ -246,6 +279,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-1416-3412
   year: '2024'
+  doi: 10.32614/CRAN.package.igraph
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -258,6 +292,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
   year: '2024'
+  doi: 10.32614/CRAN.package.knitr
 - type: software
   title: markdown
   abstract: 'markdown: Render Markdown with ''commonmark'''
@@ -274,6 +309,7 @@ references:
   - family-names: Horner
     given-names: Jeffrey
   year: '2024'
+  doi: 10.32614/CRAN.package.markdown
 - type: software
   title: rsvg
   abstract: 'rsvg: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or
@@ -287,6 +323,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-4035-0289
   year: '2024'
+  doi: 10.32614/CRAN.package.rsvg
 - type: software
   title: svglite
   abstract: 'svglite: An ''SVG'' Graphics Device'
@@ -314,6 +351,7 @@ references:
     given-names: Vaudor
     email: [email protected]
   year: '2024'
+  doi: 10.32614/CRAN.package.svglite
 - type: software
   title: tinysnapshot
   abstract: 'tinysnapshot: Snapshots for Unit Tests using the ''tinytest'' Framework'
@@ -326,6 +364,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0003-2042-7063
   year: '2024'
+  doi: 10.32614/CRAN.package.tinysnapshot
 - type: software
   title: tinytest
   abstract: 'tinytest: Lightweight and Feature Complete Unit Testing Framework'
@@ -339,14 +378,5 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0002-9807-4686
   year: '2024'
-identifiers:
-- description: The concept DOI.
-  type: doi
-  value: 10.5281/zenodo.10225630
-- description: The versioned DOI for version 0.1.0.
-  type: doi
-  value: 10.5281/zenodo.10225631
-- description: The versioned DOI for version 0.2.0.
-  type: doi
-  value: 10.5281/zenodo.10711236
+  doi: 10.32614/CRAN.package.tinytest
 
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: nexus
 Title: Sourcing Archaeological Materials by Chemical Composition
-Version: 0.2.0.9000
+Version: 0.3.0
 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/NAMESPACE b/NAMESPACE
@@ -112,9 +112,11 @@ importFrom(methods,.valueClassTest)
 importFrom(methods,as)
 importFrom(methods,callGeneric)
 importFrom(methods,callNextMethod)
+importFrom(methods,cbind2)
 importFrom(methods,initialize)
 importFrom(methods,is)
 importFrom(methods,new)
+importFrom(methods,rbind2)
 importFrom(methods,setClass)
 importFrom(methods,setGeneric)
 importFrom(methods,setMethod)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# nexus 0.2.0.9000
+# nexus 0.3.0
 ## New classes and methods
 * Add transformation methods for `LogRatio` objects (clr <-> alr, clr -> ilr, alr -> ilr).
 * Add `condense()` to compute compositional mean of data subsets.

diff --git a/R/nexus-package.R b/R/nexus-package.R
@@ -39,8 +39,8 @@
 
 #' @import arkhe
 #' @importFrom isopleuros ternary_pairs
-#' @importFrom methods as as<- callGeneric callNextMethod
-#'  .hasSlot initialize is new setClass setGeneric setMethod slot slot<-
+#' @importFrom methods as as<- cbind2 callGeneric callNextMethod
+#'  .hasSlot initialize is new rbind2 setClass setGeneric setMethod slot slot<-
 #'  slotNames validObject .valueClassTest
 #' @importFrom MASS cov.rob
 #' @importFrom stats as.dist contr.helmert cov dist hclust mahalanobis ppoints

diff --git a/README.Rmd b/README.Rmd
@@ -20,7 +20,7 @@ Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/tesselle/nexus/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/nexus/actions)
-[![codecov](https://codecov.io/gh/tesselle/nexus/graph/badge.svg?token=3xtuBXPGiF)](https://codecov.io/gh/tesselle/nexus)
+[![codecov](https://codecov.io/gh/tesselle/nexus/graph/badge.svg?token=3xtuBXPGiF)](https://app.codecov.io/gh/tesselle/nexus)
 [![CodeFactor](https://www.codefactor.io/repository/github/tesselle/nexus/badge/main)](https://www.codefactor.io/repository/github/tesselle/nexus/overview/main)
 [![Dependencies](https://tinyverse.netlify.app/badge/nexus)](https://cran.r-project.org/package=nexus)
 

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/tesselle/nexus/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/nexus/actions)
-[![codecov](https://codecov.io/gh/tesselle/nexus/graph/badge.svg?token=3xtuBXPGiF)](https://codecov.io/gh/tesselle/nexus)
+[![codecov](https://codecov.io/gh/tesselle/nexus/graph/badge.svg?token=3xtuBXPGiF)](https://app.codecov.io/gh/tesselle/nexus)
 [![CodeFactor](https://www.codefactor.io/repository/github/tesselle/nexus/badge/main)](https://www.codefactor.io/repository/github/tesselle/nexus/overview/main)
 [![Dependencies](https://tinyverse.netlify.app/badge/nexus)](https://cran.r-project.org/package=nexus)
 
@@ -68,7 +68,7 @@ To cite nexus in publications use:
 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 0.2.0.9000,
+<https://doi.org/10.5281/zenodo.10225630>, R package version 0.3.0,
 <https://packages.tesselle.org/nexus/>.
 
 This package is a part of the tesselle project

diff --git a/codemeta.json b/codemeta.json
@@ -14,7 +14,7 @@
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.4.0 (2024-04-24)",
+  "runtimePlatform": "R version 4.4.1 (2024-06-14)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -89,7 +89,7 @@
       "@type": "SoftwareApplication",
       "identifier": "folio",
       "name": "folio",
-      "version": ">= 1.4.0",
+      "version": ">= 1.5.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -194,7 +194,7 @@
       "@type": "SoftwareApplication",
       "identifier": "dimensio",
       "name": "dimensio",
-      "version": ">= 0.8.0",
+      "version": ">= 0.9.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -207,7 +207,7 @@
       "@type": "SoftwareApplication",
       "identifier": "arkhe",
       "name": "arkhe",
-      "version": ">= 1.6.0",
+      "version": ">= 1.7.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -240,11 +240,24 @@
       "sameAs": "https://CRAN.R-project.org/package=isopleuros"
     },
     "7": {
+      "@type": "SoftwareApplication",
+      "identifier": "khroma",
+      "name": "khroma",
+      "version": ">= 1.14.0",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=khroma"
+    },
+    "8": {
       "@type": "SoftwareApplication",
       "identifier": "methods",
       "name": "methods"
     },
-    "8": {
+    "9": {
       "@type": "SoftwareApplication",
       "identifier": "MASS",
       "name": "MASS",
@@ -256,19 +269,19 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=MASS"
     },
-    "9": {
+    "10": {
       "@type": "SoftwareApplication",
       "identifier": "stats",
       "name": "stats"
     },
-    "10": {
+    "11": {
       "@type": "SoftwareApplication",
       "identifier": "utils",
       "name": "utils"
     },
     "SystemRequirements": null
   },
-  "fileSize": "804.818KB",
+  "fileSize": "992.587KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -295,7 +308,7 @@
   ],
   "releaseNotes": "https://github.com/tesselle/nexus/blob/master/NEWS.md",
   "readme": "https://github.com/tesselle/nexus/blob/main/README.md",
-  "contIntegration": ["https://github.com/tesselle/nexus/actions", "https://app.codecov.io/gh/tesselle/nexus"],
+  "contIntegration": ["https://github.com/tesselle/nexus/actions", "https://codecov.io/gh/tesselle/nexus"],
   "developmentStatus": "https://www.repostatus.org/#wip",
   "keywords": ["archaeology", "archaeological-science", "archaeometry", "provenance-studies", "compositional-data", "r-package"]
 }
diff --git a/man/figures/README-lra-2.png b/man/figures/README-lra-2.png
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,27 +1,28 @@
 # Platform
 
-|field    |value                                                                        |
-|:--------|:----------------------------------------------------------------------------|
-|version  |R version 4.3.2 (2023-10-31)                                                 |
-|os       |Ubuntu 22.04.3 LTS                                                           |
-|system   |x86_64, linux-gnu                                                            |
-|ui       |RStudio                                                                      |
-|language |(EN)                                                                         |
-|collate  |fr_FR.UTF-8                                                                  |
-|ctype    |fr_FR.UTF-8                                                                  |
-|tz       |Europe/Paris                                                                 |
-|date     |2024-02-26                                                                   |
-|rstudio  |2023.12.1+402 Ocean Storm (desktop)                                          |
-|pandoc   |3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) |
+|field    |value                                                                                |
+|:--------|:------------------------------------------------------------------------------------|
+|version  |R version 4.4.1 (2024-06-14)                                                         |
+|os       |Ubuntu 22.04.4 LTS                                                                   |
+|system   |x86_64, linux-gnu                                                                    |
+|ui       |RStudio                                                                              |
+|language |(EN)                                                                                 |
+|collate  |fr_FR.UTF-8                                                                          |
+|ctype    |fr_FR.UTF-8                                                                          |
+|tz       |Europe/Paris                                                                         |
+|date     |2024-09-03                                                                           |
+|rstudio  |2024.04.2+764 Chocolate Cosmos (desktop)                                             |
+|pandoc   |3.1.11 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/x86_64/ (via rmarkdown) |
 
 # Dependencies
 
-|package    |old   |new   |Δ  |
-|:----------|:-----|:-----|:--|
-|nexus      |0.1.0 |0.2.0 |*  |
-|arkhe      |1.6.0 |1.6.0 |   |
-|dimensio   |0.6.0 |0.6.0 |   |
-|isopleuros |1.2.0 |1.2.0 |   |
+|package    |old    |new    |Δ  |
+|:----------|:------|:------|:--|
+|nexus      |0.2.0  |0.3.0  |*  |
+|arkhe      |1.7.0  |1.7.0  |   |
+|dimensio   |0.9.0  |0.9.0  |   |
+|isopleuros |1.2.0  |1.2.0  |   |
+|khroma     |1.14.0 |1.14.0 |   |
 
 # Revdeps