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tesselle · Feb 23, 2024 · d71fb08 · d71fb08
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diff --git a/CITATION.cff b/CITATION.cff
@@ -8,13 +8,13 @@ message: 'To cite package "dimensio" in publications use:'
 type: software
 license: GPL-3.0-or-later
 title: 'dimensio: Multivariate Data Analysis'
-version: 0.5.0
+version: 0.6.0
 doi: 10.5281/zenodo.4478530
-abstract: Simple Principal Components Analysis (PCA) and (Multiple) Correspondence
+abstract: 'Simple Principal Components Analysis (PCA) and (Multiple) Correspondence
   Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides
   S4 classes and methods to compute, extract, summarize and visualize results of multivariate
   data analysis. It also includes methods for partial bootstrap validation described
-  in Greenacre (1984) <isbn:978-0-12-299050-2> and Lebart et al. (2006) <isbn:978-2-10-049616-7>.
+  in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et al. (2006, ISBN: 978-2-10-049616-7).'
 authors:
 - family-names: Frerebeau
   given-names: Nicolas
@@ -30,10 +30,10 @@ preferred-citation:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  year: '2023'
+  year: '2024'
   location:
     name: Pessac, France
-  notes: R package version 0.5.0
+  notes: R package version 0.6.0
   doi: 10.5281/zenodo.4478530
   url: https://packages.tesselle.org/dimensio/
   institution:
@@ -60,7 +60,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
   version: '>= 3.5'
@@ -76,8 +76,8 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  version: '>= 1.4.0'
-  year: '2023'
+  year: '2024'
+  version: '>= 1.6.0'
 - type: software
   title: graphics
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -86,7 +86,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -97,7 +97,7 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
 - type: software
@@ -108,44 +108,9 @@ references:
   - name: R Core Team
   location:
     name: Vienna, Austria
-  year: '2023'
+  year: '2024'
   institution:
     name: R Foundation for Statistical Computing
-- type: software
-  title: ggplot2
-  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
-  notes: Suggests
-  url: https://ggplot2.tidyverse.org
-  repository: https://CRAN.R-project.org/package=ggplot2
-  authors:
-  - family-names: Wickham
-    given-names: Hadley
-    email: [email protected]
-    orcid: https://orcid.org/0000-0003-4757-117X
-  - family-names: Chang
-    given-names: Winston
-    orcid: https://orcid.org/0000-0002-1576-2126
-  - family-names: Henry
-    given-names: Lionel
-  - family-names: Pedersen
-    given-names: Thomas Lin
-    email: [email protected]
-    orcid: https://orcid.org/0000-0002-5147-4711
-  - family-names: Takahashi
-    given-names: Kohske
-  - family-names: Wilke
-    given-names: Claus
-    orcid: https://orcid.org/0000-0002-7470-9261
-  - family-names: Woo
-    given-names: Kara
-    orcid: https://orcid.org/0000-0002-5125-4188
-  - family-names: Yutani
-    given-names: Hiroaki
-    orcid: https://orcid.org/0000-0002-3385-7233
-  - family-names: Dunnington
-    given-names: Dewey
-    orcid: https://orcid.org/0000-0002-9415-4582
-  year: '2023'
 - type: software
   title: khroma
   abstract: 'khroma: Colour Schemes for Scientific Data Visualization'
@@ -158,7 +123,7 @@ references:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  year: '2023'
+  year: '2024'
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -170,50 +135,23 @@ 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
@@ -226,7 +164,7 @@ 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'
@@ -253,7 +191,7 @@ 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'
@@ -265,7 +203,7 @@ 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'
@@ -277,7 +215,7 @@ 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
@@ -1,13 +1,13 @@
 Package: dimensio
 Title: Multivariate Data Analysis
-Version: 0.5.0.9000
+Version: 0.6.0
 Authors@R: c(
     person("Nicolas", "Frerebeau", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5759-4944", affiliation = "Université Bordeaux Montaigne")),
     person("Jean-Baptiste", "Fourvel", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0002-1061-4642", affiliation = "CNRS")),
     person("Brice", "Lebrun", , "[email protected]", role = "ctb",
-           comment = c(ORCID = "0000-0001-7503-8685", affiliation = "Université Bordeaux Montaigne")),
+           comment = c(ORCID = "0000-0001-7503-8685", "Logo designer")),
     person("Université Bordeaux Montaigne", role = "fnd"),
     person("CNRS", role = "fnd")
   )

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# dimensio 0.5.0.9000
+# dimensio 0.6.0
 ## New classes and methods
 * Add `predict()` method for MCA.
 

diff --git a/R/dimensio-package.R b/R/dimensio-package.R
@@ -2,7 +2,7 @@
 #' \tabular{ll}{
 #'  **Package:** \tab dimensio \cr
 #'  **Type:** \tab Package \cr
-#'  **Version:** \tab 0.5.0 \cr
+#'  **Version:** \tab 0.6.0 \cr
 #'  **License:** \tab GPL-3 \cr
 #'  **Zenodo:** \tab \doi{10.5281/zenodo.4478530} \cr
 #' }

diff --git a/README.Rmd b/README.Rmd
@@ -76,8 +76,7 @@ library(dimensio)
 data(iris)
 
 ## Compute PCA
-## (non numeric variables are automatically removed)
-X <- pca(iris, center = TRUE, scale = TRUE)
+X <- pca(iris, center = TRUE, scale = TRUE, sup_quali = "Species")
 ```
 
 ### Extract

diff --git a/README.md b/README.md
@@ -53,20 +53,20 @@ tools to explore the results of the analysis.
 
     To cite dimensio in publications use:
 
-      Frerebeau N (2023). _dimensio: Multivariate Data Analysis_.
+      Frerebeau N (2024). _dimensio: Multivariate Data Analysis_.
       Université Bordeaux Montaigne, Pessac, France.
       doi:10.5281/zenodo.4478530 <https://doi.org/10.5281/zenodo.4478530>,
-      R package version 0.5.0, <https://packages.tesselle.org/dimensio/>.
+      R package version 0.6.0, <https://packages.tesselle.org/dimensio/>.
 
     A BibTeX entry for LaTeX users is
 
       @Manual{,
         author = {Nicolas Frerebeau},
         title = {{dimensio: Multivariate Data Analysis}},
-        year = {2023},
+        year = {2024},
         organization = {Université Bordeaux Montaigne},
         address = {Pessac, France},
-        note = {R package version 0.5.0},
+        note = {R package version 0.6.0},
         doi = {10.5281/zenodo.4478530},
         url = {https://packages.tesselle.org/dimensio/},
       }
@@ -107,9 +107,7 @@ library(dimensio)
 data(iris)
 
 ## Compute PCA
-## (non numeric variables are automatically removed)
-X <- pca(iris, center = TRUE, scale = TRUE)
-#> 1 qualitative variable was removed: Species.
+X <- pca(iris, center = TRUE, scale = TRUE, sup_quali = "Species")
 ```
 
 ### Extract

diff --git a/codemeta.json b/codemeta.json
@@ -2,13 +2,13 @@
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@type": "SoftwareSourceCode",
   "identifier": "dimensio",
-  "description": "Simple Principal Components Analysis (PCA) and (Multiple) Correspondence Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides S4 classes and methods to compute, extract, summarize and visualize results of multivariate data analysis. It also includes methods for partial bootstrap validation described in Greenacre (1984) <isbn:978-0-12-299050-2> and Lebart et al. (2006) <isbn:978-2-10-049616-7>.",
+  "description": "Simple Principal Components Analysis (PCA) and (Multiple) Correspondence Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides S4 classes and methods to compute, extract, summarize and visualize results of multivariate data analysis. It also includes methods for partial bootstrap validation described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et al. (2006, ISBN: 978-2-10-049616-7).",
   "name": "dimensio: Multivariate Data Analysis",
   "relatedLink": ["https://packages.tesselle.org/dimensio/", "https://CRAN.R-project.org/package=dimensio"],
   "codeRepository": "https://github.com/tesselle/dimensio",
   "issueTracker": "https://github.com/tesselle/dimensio/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.5.0.9000",
+  "version": "0.6.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -66,18 +66,6 @@
     }
   ],
   "softwareSuggestions": [
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "ggplot2",
-      "name": "ggplot2",
-      "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=ggplot2"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "khroma",
@@ -104,15 +92,15 @@
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "rmarkdown",
-      "name": "rmarkdown",
+      "identifier": "markdown",
+      "name": "markdown",
       "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=rmarkdown"
+      "sameAs": "https://CRAN.R-project.org/package=markdown"
     },
     {
       "@type": "SoftwareApplication",
@@ -174,7 +162,7 @@
       "@type": "SoftwareApplication",
       "identifier": "arkhe",
       "name": "arkhe",
-      "version": ">= 1.4.0",
+      "version": ">= 1.6.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -200,11 +188,11 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1083.336KB",
+  "fileSize": "1094.783KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
-      "datePublished": "2023",
+      "datePublished": "2024",
       "author": [
         {
           "@type": "Person",
@@ -215,7 +203,7 @@
       "name": "{dimensio: Multivariate Data Analysis}",
       "identifier": "10.5281/zenodo.4478530",
       "url": "https://packages.tesselle.org/dimensio/",
-      "description": "R package version 0.5.0.9000",
+      "description": "R package version 0.6.0",
       "@id": "https://doi.org/10.5281/zenodo.4478530",
       "sameAs": "https://doi.org/10.5281/zenodo.4478530"
     }