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tesselle · Dec 10, 2024 · eff4a3c · eff4a3c
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diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ message: 'To cite package "kairos" in publications use:'
 type: software
 license: GPL-3.0-or-later
 title: 'kairos: Analysis of Chronological Patterns from Archaeological Count Data'
-version: 2.1.1
+version: 2.2.0
 doi: 10.5281/zenodo.5653896
 identifiers:
 - description: The concept DOI.
@@ -41,6 +41,9 @@ identifiers:
 - description: The versioned DOI for version 2.1.1.
   type: doi
   value: 10.5281/zenodo.12967467
+- description: The CRAN DOI
+  type: doi
+  value: 10.32614/cran.package.kairos
 - description: The Software Heritage identifier for version 1.0.1.
   type: swh
   value: swh:1:rel:508add25987e0fc9f3f29793df5578337ae2c338
@@ -54,7 +57,6 @@ authors:
   given-names: Nicolas
   email: [email protected]
   orcid: https://orcid.org/0000-0001-5759-4944
-  affiliation: Université Bordeaux Montaigne
 preferred-citation:
   type: manual
   title: 'kairos: Analysis of Chronological Patterns from Archaeological Count Data'
@@ -63,12 +65,11 @@ preferred-citation:
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
-    affiliation: Université Bordeaux Montaigne
   year: '2024'
   institution:
     name: Université Bordeaux Montaigne
     address: Pessac, France
-  notes: R package version 2.1.1
+  notes: R package version 2.2.0
   url: https://packages.tesselle.org/kairos/
   doi: 10.5281/zenodo.5653896
 repository: https://CRAN.R-project.org/package=kairos
@@ -79,7 +80,6 @@ contact:
   given-names: Nicolas
   email: [email protected]
   orcid: https://orcid.org/0000-0001-5759-4944
-  affiliation: Université Bordeaux Montaigne
 keywords:
 - chronology
 - matrix seriation
@@ -109,30 +109,27 @@ references:
     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.dimensio
-  version: '>= 0.8.0'
+  version: '>= 0.10.1'
 - type: software
   title: aion
   abstract: 'aion: Archaeological Time Series'
   notes: Imports
   url: https://packages.tesselle.org/aion/
-  repository: https://tesselle.r-universe.dev
+  repository: https://CRAN.R-project.org/package=aion
   authors:
   - family-names: Frerebeau
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
-    affiliation: Université Bordeaux Montaigne
   - family-names: Roe
     given-names: Joe
     email: [email protected]
     orcid: https://orcid.org/0000-0002-1011-1244
-    affiliation: Universität Bern
   year: '2024'
   doi: 10.32614/CRAN.package.aion
-  version: '>= 1.0.4'
+  version: '>= 1.3.0'
 - type: software
   title: arkhe
   abstract: 'arkhe: Tools for Cleaning Rectangular Data'
@@ -144,10 +141,9 @@ references:
     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.arkhe
-  version: '>= 1.6.0'
+  version: '>= 1.9.0'
 - type: software
   title: extraDistr
   abstract: 'extraDistr: Additional Univariate and Multivariate Distributions'
@@ -169,7 +165,6 @@ references:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
   year: '2024'
-  doi: 10.32614/CRAN.package.grDevices
 - type: software
   title: methods
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -180,7 +175,6 @@ references:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
   year: '2024'
-  doi: 10.32614/CRAN.package.methods
 - type: software
   title: stats
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -191,7 +185,6 @@ references:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
   year: '2024'
-  doi: 10.32614/CRAN.package.stats
 - type: software
   title: utils
   abstract: 'R: A Language and Environment for Statistical Computing'
@@ -202,7 +195,6 @@ references:
     name: R Foundation for Statistical Computing
     address: Vienna, Austria
   year: '2024'
-  doi: 10.32614/CRAN.package.utils
 - type: software
   title: folio
   abstract: 'folio: Datasets for Teaching Archaeology and Paleontology'
@@ -217,7 +209,7 @@ references:
     affiliation: Université Bordeaux Montaigne
   year: '2024'
   doi: 10.32614/CRAN.package.folio
-  version: '>= 1.4.0'
+  version: '>= 1.5.0'
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -258,7 +250,7 @@ references:
   authors:
   - family-names: Ooms
     given-names: Jeroen
-    email: [email protected]
+    email: [email protected]
     orcid: https://orcid.org/0000-0002-4035-0289
   year: '2024'
   doi: 10.32614/CRAN.package.rsvg
@@ -304,7 +296,7 @@ references:
     affiliation: Université Bordeaux Montaigne
   year: '2024'
   doi: 10.32614/CRAN.package.tabula
-  version: '>= 3.1.0'
+  version: '>= 3.1.1'
 - type: software
   title: tinysnapshot
   abstract: 'tinysnapshot: Snapshots for Unit Tests using the ''tinytest'' Framework'

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
 Package: kairos
 Title: Analysis of Chronological Patterns from Archaeological Count Data
-Version: 2.1.1.9000
+Version: 2.2.0
 Authors@R: c(
     person("Nicolas", "Frerebeau", , "[email protected]", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-5759-4944", affiliation = "Université Bordeaux Montaigne")),
+           comment = c(ORCID = "0000-0001-5759-4944")),
     person("Brice", "Lebrun", , "[email protected]", role = "ctb",
            comment = c(ORCID = "0000-0001-7503-8685", "Logo designer")),
     person("Ben", "Marwick", , "[email protected]", role = "ctb",
-           comment = c(ORCID = "0000-0001-7879-4531", affiliation = "University of Washington")),
+           comment = c(ORCID = "0000-0001-7879-4531")),
     person("Anne", "Philippe", , "[email protected]", role = "ctb",
-           comment = c(ORCID = "0000-0002-5331-5087", affiliation = "Université de Nantes")),
+           comment = c(ORCID = "0000-0002-5331-5087")),
     person("Université Bordeaux Montaigne", role = "fnd"),
     person("CNRS", role = "fnd")
   )

diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,18 @@
-# kairos 2.1.1.9000
+# kairos 2.2.0
+## New classes and methods
+* Add `as_seriation()` to coerce objects to seriation orders.
+* Add `assess()` to test the significance of seriation solutions (#4).
+* Add `density_event()` and `density_accumulation()` to compute density estimates of event and accumulation dates.
+* Add `order_rows()` and `order_columns()` to get permutation order.
+* Add `refine()` to refine CA-based seriation.
+
+## Enhancements
+* Translate into French.
+
 ## Bugfixes & changes
 * Fix a bug in `predict_event()` and `predict_accumulation()`: supplementary rows are no longer ignored.
+* Fix calendar in `jackknife()` and `bootstrap()` methods for `EventDate-class`.
+* Deprecate `get_order()` and `seriate_refine()`.
 
 # kairos 2.1.1
 ## Internals

diff --git a/R/kairos-package.R b/R/kairos-package.R
@@ -2,7 +2,7 @@
 #' \tabular{ll}{
 #'  **Package:** \tab kairos \cr
 #'  **Type:** \tab Package \cr
-#'  **Version:** \tab 2.1.1 \cr
+#'  **Version:** \tab 2.2.0 \cr
 #'  **License:** \tab GPL-3 \cr
 #' }
 #'

diff --git a/README.md b/README.md
@@ -63,7 +63,7 @@ To cite kairos in publications use:
 Frerebeau N (2024). *kairos: Analysis of Chronological Patterns from
 Archaeological Count Data*. Université Bordeaux Montaigne, Pessac,
 France. <doi:10.5281/zenodo.5653896>
-<https://doi.org/10.5281/zenodo.5653896>, R package version 2.1.1,
+<https://doi.org/10.5281/zenodo.5653896>, R package version 2.2.0,
 <https://packages.tesselle.org/kairos/>.
 
 This package is a part of the tesselle project

diff --git a/codemeta.json b/codemeta.json
@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/tesselle/kairos",
   "issueTracker": "https://github.com/tesselle/kairos/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "2.1.1",
+  "version": "2.2.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.4.1 (2024-06-14)",
+  "runtimePlatform": "R version 4.4.2 (2024-10-31)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -77,7 +77,7 @@
       "@type": "SoftwareApplication",
       "identifier": "folio",
       "name": "folio",
-      "version": ">= 1.4.0",
+      "version": ">= 1.5.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -138,7 +138,7 @@
       "@type": "SoftwareApplication",
       "identifier": "tabula",
       "name": "tabula",
-      "version": ">= 3.1.0",
+      "version": ">= 3.1.1",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -183,7 +183,7 @@
       "@type": "SoftwareApplication",
       "identifier": "dimensio",
       "name": "dimensio",
-      "version": ">= 0.8.0",
+      "version": ">= 0.10.1",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -196,7 +196,7 @@
       "@type": "SoftwareApplication",
       "identifier": "aion",
       "name": "aion",
-      "version": ">= 1.0.4",
+      "version": ">= 1.3.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -209,7 +209,7 @@
       "@type": "SoftwareApplication",
       "identifier": "arkhe",
       "name": "arkhe",
-      "version": ">= 1.6.0",
+      "version": ">= 1.9.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -252,7 +252,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "707.351KB",
+  "fileSize": "995.258KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -267,7 +267,7 @@
       "name": "{kairos: Analysis of Chronological Patterns from Archaeological Count Data}",
       "identifier": "10.5281/zenodo.5653896",
       "url": "https://packages.tesselle.org/kairos/",
-      "description": "R package version 2.1.1",
+      "description": "R package version 2.2.0",
       "@id": "https://doi.org/10.5281/zenodo.5653896",
       "sameAs": "https://doi.org/10.5281/zenodo.5653896"
     }

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,5 +1,5 @@
 ## Test environments
-* Local R installation: R 4.4.1
+* Local R installation: R 4.4.2
 * Ubuntu (on GitHub Actions): R devel, release, oldrel
 * Windows (on GitHub Actions and win-builder): R devel, release, oldrel
 * MacOS (on GitHub Actions): R release

diff --git a/man/kairos-package.Rd b/man/kairos-package.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,29 +1,29 @@
 # 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   |NA                                  |
+|field    |value                        |
+|:--------|:----------------------------|
+|version  |R version 4.4.2 (2024-10-31) |
+|os       |Ubuntu 22.04.5 LTS           |
+|system   |x86_64, linux-gnu            |
+|ui       |X11                          |
+|language |(EN)                         |
+|collate  |fr_FR.UTF-8                  |
+|ctype    |fr_FR.UTF-8                  |
+|tz       |Europe/Paris                 |
+|date     |2024-12-10                   |
+|pandoc   |NA                           |
 
 # Dependencies
 
-|package    |old    |new    |Δ  |
-|:----------|:------|:------|:--|
-|kairos     |2.0.2  |2.1.0  |*  |
-|aion       |1.0.2  |1.0.2  |   |
-|arkhe      |1.6.0  |1.6.0  |   |
-|dimensio   |0.6.0  |0.6.0  |   |
-|extraDistr |1.10.0 |1.10.0 |   |
-|Rcpp       |1.0.12 |1.0.12 |   |
+|package    |old      |new      |Δ  |
+|:----------|:--------|:--------|:--|
+|kairos     |2.1.1    |2.2.0    |*  |
+|aion       |1.3.0    |1.3.0    |   |
+|arkhe      |1.9.0    |1.9.0    |   |
+|dimensio   |0.10.1   |0.10.1   |   |
+|extraDistr |1.10.0   |1.10.0   |   |
+|khroma     |1.14.0   |1.14.0   |   |
+|Rcpp       |1.0.13-1 |1.0.13-1 |   |
 
 # Revdeps