Prepare for next release

CITATION.cff

@@ -1,5 +1,5 @@
 # -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v0.2.2
+# CITATION file created with {cffr} R package, v0.3.0
 # See also: https://docs.ropensci.org/cffr/
 # -----------------------------------------------------------
 
@@ -8,12 +8,13 @@ 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: 1.1.0.9000
-abstract: A toolkit for absolute dating and analysis of chronological patterns. This
-  package includes functions for chronological modeling and dating of archaeological
-  assemblages from count data. It provides methods for matrix seriation. It also allows
-  to compute time point estimates and density estimates of the occupation and duration
-  of an archaeological site.
+version: 1.2.0
+doi: 10.5281/zenodo.5653896
+abstract: A toolkit for absolute and relative dating and analysis of chronological
+  patterns. This package includes functions for chronological modeling and dating
+  of archaeological assemblages from count data. It provides methods for matrix seriation.
+  It also allows to compute time point estimates and density estimates of the occupation
+  and duration of an archaeological site.
 authors:
 - family-names: Frerebeau
   given-names: Nicolas
@@ -29,28 +30,14 @@ preferred-citation:
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  version: 1.1.0.9000
-  abstract: A toolkit for absolute dating and analysis of chronological patterns.
-    This package includes functions for chronological modeling and dating of archaeological
-    assemblages from count data. It provides methods for matrix seriation. It also
-    allows to compute time point estimates and density estimates of the occupation
-    and duration of an archaeological site.
-  repository: https://CRAN.R-project.org/package=kairos
-  repository-code: https://github.com/tesselle/kairos
-  url: https://packages.tesselle.org/kairos/
-  contact:
-  - family-names: Frerebeau
-    given-names: Nicolas
-    email: [email protected]
-    orcid: https://orcid.org/0000-0001-5759-4944
-    affiliation: Université Bordeaux Montaigne
-  keywords:
-  - archaeological-science
-  - archaeology
-  - chronology
-  - r-package
-  license: GPL-3.0-or-later
   year: '2022'
+  location:
+    name: Pessac, France
+  notes: R package version 1.2.0
+  url: https://packages.tesselle.org/kairos/
+  doi: 10.5281/zenodo.5653896
+  institution:
+    name: Université Bordeaux Montaigne
 repository: https://CRAN.R-project.org/package=kairos
 repository-code: https://github.com/tesselle/kairos
 url: https://packages.tesselle.org/kairos/
@@ -62,6 +49,7 @@ contact:
   affiliation: Université Bordeaux Montaigne
 keywords:
 - chronology
+- matrix seriation
 - archaeology
 - archaeological science
 - r package
@@ -80,7 +68,7 @@ references:
   version: '>= 3.4'
 - type: software
   title: arkhe
-  abstract: 'arkhe: Representation of Archaeological Data'
+  abstract: 'arkhe: Tools for Cleaning Rectangular Data'
   notes: Imports
   authors:
   - family-names: Frerebeau
@@ -90,20 +78,7 @@ references:
     affiliation: Université Bordeaux Montaigne
   year: '2022'
   url: https://CRAN.R-project.org/package=arkhe
-  version: '>= 0.5.0'
-- type: software
-  title: boot
-  abstract: 'boot: Bootstrap Functions (Originally by Angelo Canty for S)'
-  notes: Imports
-  authors:
-  - family-names: Canty
-    given-names: Angelo
-    email: [email protected]
-  - family-names: Ripley
-    given-names: Brian
-    email: [email protected]
-  year: '2022'
-  url: https://CRAN.R-project.org/package=boot
+  version: '>= 1.0.0'
 - type: software
   title: dimensio
   abstract: 'dimensio: Multivariate Data Analysis'
@@ -113,9 +88,9 @@ references:
     given-names: Nicolas
     email: [email protected]
     orcid: https://orcid.org/0000-0001-5759-4944
+    affiliation: Université Bordeaux Montaigne
+  version: '>= 0.3.0'
   year: '2022'
-  url: https://CRAN.R-project.org/package=dimensio
-  version: '>= 0.2.2'
 - type: software
   title: extraDistr
   abstract: 'extraDistr: Additional Univariate and Multivariate Distributions'
@@ -159,6 +134,18 @@ references:
     orcid: https://orcid.org/0000-0002-9415-4582
   year: '2022'
   url: https://CRAN.R-project.org/package=ggplot2
+- type: software
+  title: grDevices
+  abstract: 'R: A Language and Environment for Statistical Computing'
+  notes: Imports
+  authors:
+  - name: R Core Team
+  location:
+    name: Vienna, Austria
+  year: '2022'
+  url: https://www.R-project.org/
+  institution:
+    name: R Foundation for Statistical Computing
 - type: software
   title: Hmisc
   abstract: 'Hmisc: Harrell Miscellaneous'
@@ -241,6 +228,7 @@ references:
     affiliation: Université Bordeaux Montaigne
   year: '2022'
   url: https://CRAN.R-project.org/package=folio
+  version: '>= 1.3.0'
 - type: software
   title: khroma
   abstract: 'khroma: Colour Schemes for Scientific Data Visualization'
@@ -303,6 +291,18 @@ references:
     orcid: https://orcid.org/0000-0003-3925-190X
   year: '2022'
   url: https://CRAN.R-project.org/package=rmarkdown
+- type: software
+  title: tabula
+  abstract: 'tabula: Analysis and Visualization of Archaeological Count Data'
+  notes: Suggests
+  authors:
+  - family-names: Frerebeau
+    given-names: Nicolas
+    email: [email protected]
+    orcid: https://orcid.org/0000-0001-5759-4944
+    affiliation: Université Bordeaux Montaigne
+  version: '>= 2.0.0'
+  year: '2022'
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: kairos
 Title: Analysis of Chronological Patterns from Archaeological Count Data
-Version: 1.1.0.9000
+Version: 1.2.0
 Authors@R: 
     c(person(given = "Nicolas",
              family = "Frerebeau",

NEWS.md

@@ -1,4 +1,4 @@
-# kairos 1.1.0.9000
+# kairos 1.2.0
 ## New classes and methods
 * Add `seriate_refine()` method for `PermutationOrder` objects.
 

R/kairos-package.R

@@ -2,7 +2,7 @@
 #' \tabular{ll}{
 #'  **Package:** \tab kairos \cr
 #'  **Type:** \tab Package \cr
-#'  **Version:** \tab 1.1.0 \cr
+#'  **Version:** \tab 1.2.0 \cr
 #'  **License:** \tab GPL-3 \cr
 #' }
 #'

codemeta.json

@@ -2,19 +2,19 @@
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@type": "SoftwareSourceCode",
   "identifier": "kairos",
-  "description": "A toolkit for absolute dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site.",
+  "description": "A toolkit for absolute and relative dating and analysis of chronological patterns. This package includes functions for chronological modeling and dating of archaeological assemblages from count data. It provides methods for matrix seriation. It also allows to compute time point estimates and density estimates of the occupation and duration of an archaeological site.",
   "name": "kairos: Analysis of Chronological Patterns from Archaeological Count Data",
   "relatedLink": ["https://packages.tesselle.org/kairos/", "https://CRAN.R-project.org/package=kairos"],
   "codeRepository": "https://github.com/tesselle/kairos",
   "issueTracker": "https://github.com/tesselle/kairos/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "1.1.0.9000",
+  "version": "1.2.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.2.0 (2022-04-22)",
+  "runtimePlatform": "R version 4.2.2 (2022-10-31)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -79,6 +79,7 @@
       "@type": "SoftwareApplication",
       "identifier": "folio",
       "name": "folio",
+      "version": ">= 1.3.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -123,6 +124,19 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "tabula",
+      "name": "tabula",
+      "version": ">= 2.0.0",
+      "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=tabula"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "testthat",
@@ -161,7 +175,7 @@
       "@type": "SoftwareApplication",
       "identifier": "arkhe",
       "name": "arkhe",
-      "version": ">= 0.5.0",
+      "version": ">= 1.0.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -171,22 +185,10 @@
       "sameAs": "https://CRAN.R-project.org/package=arkhe"
     },
     "3": {
-      "@type": "SoftwareApplication",
-      "identifier": "boot",
-      "name": "boot",
-      "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=boot"
-    },
-    "4": {
       "@type": "SoftwareApplication",
       "identifier": "dimensio",
       "name": "dimensio",
-      "version": ">= 0.2.2",
+      "version": ">= 0.3.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -195,7 +197,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=dimensio"
     },
-    "5": {
+    "4": {
       "@type": "SoftwareApplication",
       "identifier": "extraDistr",
       "name": "extraDistr",
@@ -207,7 +209,7 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=extraDistr"
     },
-    "6": {
+    "5": {
       "@type": "SoftwareApplication",
       "identifier": "ggplot2",
       "name": "ggplot2",
@@ -219,6 +221,11 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=ggplot2"
     },
+    "6": {
+      "@type": "SoftwareApplication",
+      "identifier": "grDevices",
+      "name": "grDevices"
+    },
     "7": {
       "@type": "SoftwareApplication",
       "identifier": "Hmisc",
@@ -260,7 +267,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "811.74KB",
+  "fileSize": "834.823KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -275,7 +282,7 @@
       "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 1.1.0",
+      "description": "R package version 1.2.0",
       "@id": "https://doi.org/10.5281/zenodo.5653896",
       "sameAs": "https://doi.org/10.5281/zenodo.5653896"
     }
@@ -284,5 +291,5 @@
   "readme": "https://github.com/tesselle/kairos/blob/main/README.md",
   "contIntegration": ["https://github.com/tesselle/kairos/actions", "https://app.codecov.io/gh/tesselle/kairos"],
   "developmentStatus": "https://www.repostatus.org/#active",
-  "keywords": ["r-package", "archaeology", "archaeological-science", "chronology"]
+  "keywords": ["r-package", "archaeology", "archaeological-science", "chronology", "matrix-seriation"]
 }

cran-comments.md

@@ -8,7 +8,6 @@
 
 0 errors | 1 warnings | 1 note
 
-* CRAN package check warnings ("multiple methods tables") and notes ("Namespace in Imports field not imported") have been fixed.
 * Some links in the documentation point to articles behind paywalls that may return an error.
 
 ## revdepcheck results

inst/CITATION

@@ -7,14 +7,14 @@ citEntry(
   year         = "2022",
   organization = "Université Bordeaux Montaigne",
   address      = "Pessac, France",
-  note         = "R package version 1.1.0",
+  note         = "R package version 1.2.0",
   url          = "https://packages.tesselle.org/kairos/",
   doi          = "10.5281/zenodo.5653896",
 
   textVersion  =
   paste("Frerebeau, Nicolas (2022).",
         "kairos: Analysis of Chronological Patterns from Archaeological Count Data.",
-        "R package version 1.1.0",
+        "R package version 1.2.0",
         "Université Bordeaux Montaigne, Pessac, France.",
         "DOI 10.5281/zenodo.5653896.",
         "URL https://packages.tesselle.org/kairos.")