From 249ea09466b3ae5c2ddc26d5a6fee12d99914a44 Mon Sep 17 00:00:00 2001 From: nfrerebeau Date: Tue, 8 Nov 2022 18:27:06 +0100 Subject: [PATCH] Prepare for next release --- CITATION.cff | 90 +++++++++++++-------------- DESCRIPTION | 2 +- NEWS.md | 2 +- R/kairos-package.R | 2 +- codemeta.json | 51 ++++++++------- cran-comments.md | 1 - inst/CITATION | 4 +- man/kairos-package.Rd | 2 +- revdep/README.md | 141 +++++++++++++++++++++--------------------- 9 files changed, 151 insertions(+), 144 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 2360ee9..e8d9919 100644 --- a/CITATION.cff +++ b/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: nicolas.frerebeau@u-bordeaux-montaigne.fr 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: nicolas.frerebeau@u-bordeaux-montaigne.fr - 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: cantya@mcmaster.ca - - family-names: Ripley - given-names: Brian - email: ripley@stats.ox.ac.uk - 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: nicolas.frerebeau@u-bordeaux-montaigne.fr 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: nicolas.frerebeau@u-bordeaux-montaigne.fr + 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' diff --git a/DESCRIPTION b/DESCRIPTION index 111e8c2..bb2232d 100644 --- a/DESCRIPTION +++ b/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", diff --git a/NEWS.md b/NEWS.md index 8bf3d05..f61ca08 100644 --- a/NEWS.md +++ b/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. diff --git a/R/kairos-package.R b/R/kairos-package.R index a6f5c12..15ddfc6 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 1.1.0 \cr +#' **Version:** \tab 1.2.0 \cr #' **License:** \tab GPL-3 \cr #' } #' diff --git a/codemeta.json b/codemeta.json index 9f8f740..afd33f7 100644 --- a/codemeta.json +++ b/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"] } diff --git a/cran-comments.md b/cran-comments.md index b85b8a3..c67d88e 100644 --- a/cran-comments.md +++ b/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 diff --git a/inst/CITATION b/inst/CITATION index 03eb9bd..cc090dc 100644 --- a/inst/CITATION +++ b/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.") diff --git a/man/kairos-package.Rd b/man/kairos-package.Rd index ed68f5b..a82ca12 100644 --- a/man/kairos-package.Rd +++ b/man/kairos-package.Rd @@ -15,7 +15,7 @@ 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 1.1.0 \cr +\strong{Version:} \tab 1.2.0 \cr \strong{License:} \tab GPL-3 \cr } } diff --git a/revdep/README.md b/revdep/README.md index 391bb83..fce149b 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,78 +1,79 @@ # Platform -|field |value | -|:--------|:-----------------------------------------------------------| -|version |R version 4.2.0 (2022-04-22) | -|os |Ubuntu 20.04.4 LTS | -|system |x86_64, linux-gnu | -|ui |RStudio | -|language |(EN) | -|collate |fr_FR.UTF-8 | -|ctype |fr_FR.UTF-8 | -|tz |Europe/Paris | -|date |2022-06-17 | -|rstudio |2022.02.3+492 Prairie Trillium (desktop) | -|pandoc |2.17.1.1 @ /usr/lib/rstudio/bin/quarto/bin/ (via rmarkdown) | +|field |value | +|:--------|:-------------------------------------------------------------| +|version |R version 4.2.2 (2022-10-31) | +|os |Ubuntu 20.04.5 LTS | +|system |x86_64, linux-gnu | +|ui |RStudio | +|language |(EN) | +|collate |fr_FR.UTF-8 | +|ctype |fr_FR.UTF-8 | +|tz |Europe/Paris | +|date |2022-11-08 | +|rstudio |2022.07.1+554 Spotted Wakerobin (desktop) | +|pandoc |2.18 @ /usr/lib/rstudio/bin/quarto/bin/tools/ (via rmarkdown) | # Dependencies -|package |old |new |Δ | -|:------------|:-------|:-------|:--| -|kairos |1.0.1 |1.1.0 |* | -|arkhe |0.5.0 |0.5.0 | | -|backports |1.4.1 |1.4.1 | | -|base64enc |0.1-3 |0.1-3 | | -|checkmate |2.1.0 |2.1.0 | | -|cli |3.3.0 |3.3.0 | | -|colorspace |2.0-3 |2.0-3 | | -|crayon |1.5.1 |1.5.1 | | -|data.table |1.14.2 |1.14.2 | | -|digest |0.6.29 |0.6.29 | | -|dimensio |0.2.2 |0.2.2 | | -|ellipsis |0.3.2 |0.3.2 | | -|evaluate |0.15 |0.15 | | -|extraDistr |1.9.1 |1.9.1 | | -|fansi |1.0.3 |1.0.3 | | -|farver |2.1.0 |2.1.0 | | -|fastmap |1.1.0 |1.1.0 | | -|Formula |1.2-4 |1.2-4 | | -|ggplot2 |3.3.6 |3.3.6 | | -|glue |1.6.2 |1.6.2 | | -|gridExtra |2.3 |2.3 | | -|gtable |0.3.0 |0.3.0 | | -|highr |0.9 |0.9 | | -|Hmisc |4.7-0 |4.7-0 | | -|htmlTable |2.4.0 |2.4.0 | | -|htmltools |0.5.2 |0.5.2 | | -|htmlwidgets |1.5.4 |1.5.4 | | -|isoband |0.2.5 |0.2.5 | | -|jpeg |0.1-9 |0.1-9 | | -|jsonlite |1.8.0 |1.8.0 | | -|knitr |1.39 |1.39 | | -|labeling |0.4.2 |0.4.2 | | -|latticeExtra |0.6-29 |0.6-29 | | -|lifecycle |1.0.1 |1.0.1 | | -|magrittr |2.0.3 |2.0.3 | | -|munsell |0.5.0 |0.5.0 | | -|pillar |1.7.0 |1.7.0 | | -|pkgconfig |2.0.3 |2.0.3 | | -|png |0.1-7 |0.1-7 | | -|R6 |2.5.1 |2.5.1 | | -|RColorBrewer |1.1-3 |1.1-3 | | -|Rcpp |1.0.8.3 |1.0.8.3 | | -|rlang |1.0.2 |1.0.2 | | -|rstudioapi |0.13 |0.13 | | -|scales |1.2.0 |1.2.0 | | -|stringi |1.7.6 |1.7.6 | | -|stringr |1.4.0 |1.4.0 | | -|tibble |3.1.7 |3.1.7 | | -|utf8 |1.2.2 |1.2.2 | | -|vctrs |0.4.1 |0.4.1 | | -|viridis |0.6.2 |0.6.2 | | -|viridisLite |0.4.0 |0.4.0 | | -|withr |2.5.0 |2.5.0 | | -|xfun |0.31 |0.31 | | -|yaml |2.3.5 |2.3.5 | | +|package |old |new |Δ | +|:------------|:---------|:---------|:--| +|kairos |1.1.0 |1.2.0 |* | +|arkhe |1.0.0 |1.0.0 | | +|backports |1.4.1 |1.4.1 | | +|base64enc |0.1-3 |0.1-3 | | +|checkmate |2.1.0 |2.1.0 | | +|cli |3.4.1 |3.4.1 | | +|colorspace |2.0-3 |2.0-3 | | +|data.table |1.14.4 |1.14.4 | | +|deldir |1.0-6 |1.0-6 | | +|digest |0.6.30 |0.6.30 | | +|dimensio |0.3.0 |0.3.0 | | +|evaluate |0.18 |0.18 | | +|extraDistr |1.9.1 |1.9.1 | | +|fansi |1.0.3 |1.0.3 | | +|farver |2.1.1 |2.1.1 | | +|fastmap |1.1.0 |1.1.0 | | +|Formula |1.2-4 |1.2-4 | | +|ggplot2 |3.4.0 |3.4.0 | | +|glue |1.6.2 |1.6.2 | | +|gridExtra |2.3 |2.3 | | +|gtable |0.3.1 |0.3.1 | | +|highr |0.9 |0.9 | | +|Hmisc |4.7-1 |4.7-1 | | +|htmlTable |2.4.1 |2.4.1 | | +|htmltools |0.5.3 |0.5.3 | | +|htmlwidgets |1.5.4 |1.5.4 | | +|interp |1.1-3 |1.1-3 | | +|isoband |0.2.6 |0.2.6 | | +|jpeg |0.1-9 |0.1-9 | | +|jsonlite |1.8.3 |1.8.3 | | +|knitr |1.40 |1.40 | | +|labeling |0.4.2 |0.4.2 | | +|latticeExtra |0.6-30 |0.6-30 | | +|lifecycle |1.0.3 |1.0.3 | | +|magrittr |2.0.3 |2.0.3 | | +|munsell |0.5.0 |0.5.0 | | +|pillar |1.8.1 |1.8.1 | | +|pkgconfig |2.0.3 |2.0.3 | | +|png |0.1-7 |0.1-7 | | +|R6 |2.5.1 |2.5.1 | | +|RColorBrewer |1.1-3 |1.1-3 | | +|Rcpp |1.0.9 |1.0.9 | | +|RcppEigen |0.3.3.9.3 |0.3.3.9.3 | | +|rlang |1.0.6 |1.0.6 | | +|rstudioapi |0.14 |0.14 | | +|scales |1.2.1 |1.2.1 | | +|stringi |1.7.8 |1.7.8 | | +|stringr |1.4.1 |1.4.1 | | +|tibble |3.1.8 |3.1.8 | | +|utf8 |1.2.2 |1.2.2 | | +|vctrs |0.5.0 |0.5.0 | | +|viridis |0.6.2 |0.6.2 | | +|viridisLite |0.4.1 |0.4.1 | | +|withr |2.5.0 |2.5.0 | | +|xfun |0.34 |0.34 | | +|yaml |2.3.6 |2.3.6 | | # Revdeps