From eff4a3c6864f40b7661a7d3372b3494e4dd00a00 Mon Sep 17 00:00:00 2001 From: nfrerebeau Date: Tue, 10 Dec 2024 12:26:58 +0100 Subject: [PATCH] Prepare for next release --- CITATION.cff | 32 ++++++++++++-------------------- DESCRIPTION | 8 ++++---- NEWS.md | 14 +++++++++++++- R/kairos-package.R | 2 +- README.md | 2 +- codemeta.json | 18 +++++++++--------- cran-comments.md | 2 +- man/kairos-package.Rd | 2 +- revdep/README.md | 42 +++++++++++++++++++++--------------------- 9 files changed, 63 insertions(+), 59 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 96a49fa..df43e51 100644 --- 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: nicolas.frerebeau@u-bordeaux-montaigne.fr 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: nicolas.frerebeau@u-bordeaux-montaigne.fr 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: nicolas.frerebeau@u-bordeaux-montaigne.fr 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: nicolas.frerebeau@u-bordeaux-montaigne.fr 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: nicolas.frerebeau@u-bordeaux-montaigne.fr orcid: https://orcid.org/0000-0001-5759-4944 - affiliation: Université Bordeaux Montaigne - family-names: Roe given-names: Joe email: joseph.roe@iaw.unibe.ch 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: nicolas.frerebeau@u-bordeaux-montaigne.fr 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: jeroen@berkeley.edu + email: jeroenooms@gmail.com 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 index c1ad404..bccff4d 100644 --- 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", , "nicolas.frerebeau@u-bordeaux-montaigne.fr", 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", , "brice.lebrun@u-bordeaux-montaigne.fr", role = "ctb", comment = c(ORCID = "0000-0001-7503-8685", "Logo designer")), person("Ben", "Marwick", , "bmarwick@uw.edu", role = "ctb", - comment = c(ORCID = "0000-0001-7879-4531", affiliation = "University of Washington")), + comment = c(ORCID = "0000-0001-7879-4531")), person("Anne", "Philippe", , "anne.philippe@univ-nantes.fr", 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 index 88ba503..a14150b 100644 --- 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 index 107d35f..6d86a53 100644 --- 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 index 0d41e73..e9c2cc6 100644 --- 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. -, R package version 2.1.1, +, R package version 2.2.0, . This package is a part of the tesselle project diff --git a/codemeta.json b/codemeta.json index 6b6eac1..ab971d0 100644 --- 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 index 2391e2e..3e285e3 100644 --- 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 index 2968e81..67cdaac 100644 --- a/man/kairos-package.Rd +++ b/man/kairos-package.Rd @@ -14,7 +14,7 @@ A toolkit for absolute and relative dating and analysis of chronological pattern \tabular{ll}{ \strong{Package:} \tab kairos \cr \strong{Type:} \tab Package \cr -\strong{Version:} \tab 2.1.1 \cr +\strong{Version:} \tab 2.2.0 \cr \strong{License:} \tab GPL-3 \cr } } diff --git a/revdep/README.md b/revdep/README.md index bdf07a8..d2b9af8 100644 --- 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