diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 54797a1..03208fd 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -16,11 +16,11 @@ If you want to make a bigger change, it's a good idea to first file an issue and * Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. * Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`. * Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser. The title of your PR should briefly describe the change. The body of your PR should contain `Fixes #issue-number`. -* For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in . +* For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in . ### Code style -* New code should follow the [style guide](https://documentation.tesselle.org). +* New code should follow the [style guide](https://www.tesselle.org/style.html). * We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation. * We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. Contributions with test cases included are easier to accept. diff --git a/CITATION.cff b/CITATION.cff index efc0795..7096168 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,5 @@ # ----------------------------------------------------------- -# CITATION file created with {cffr} R package, v0.1.0 +# CITATION file created with {cffr} R package, v0.2.1 # See also: https://docs.ropensci.org/cffr/ # ----------------------------------------------------------- @@ -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: 1.0.0.9000 +version: 1.0.1 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 allows to compute time point estimates and density @@ -28,7 +28,7 @@ preferred-citation: email: nicolas.frerebeau@u-bordeaux-montaigne.fr orcid: https://orcid.org/0000-0001-5759-4944 affiliation: Université Bordeaux Montaigne - version: 1.0.0.9000 + version: 1.0.1 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 allows to compute time point estimates and density @@ -41,8 +41,13 @@ preferred-citation: 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: '2021' + year: '2022' repository-code: https://github.com/tesselle/kairos url: https://packages.tesselle.org/kairos/ contact: @@ -56,6 +61,252 @@ keywords: - archaeology - archaeological science - r package +references: +- type: software + title: 'R: A Language and Environment for Statistical Computing' + notes: Depends + authors: + - name: R Core Team + location: + name: Vienna, Austria + year: '2022' + url: https://www.R-project.org/ + institution: + name: R Foundation for Statistical Computing + version: '>= 3.4' +- type: software + title: arkhe + abstract: 'arkhe: Representation of Archaeological Data' + notes: Imports + authors: + - family-names: Frerebeau + given-names: Nicolas + email: nicolas.frerebeau@u-bordeaux-montaigne.fr + orcid: https://orcid.org/0000-0001-5759-4944 + year: '2022' + url: https://CRAN.R-project.org/package=arkhe + version: '>= 0.4.0' +- type: software + title: dimensio + abstract: 'dimensio: Multivariate Data Analysis' + notes: Imports + authors: + - family-names: Frerebeau + given-names: Nicolas + email: nicolas.frerebeau@u-bordeaux-montaigne.fr + orcid: https://orcid.org/0000-0001-5759-4944 + 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' + notes: Imports + authors: + - family-names: Wolodzko + given-names: Tymoteusz + year: '2022' + url: https://CRAN.R-project.org/package=extraDistr +- type: software + title: ggplot2 + abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics' + notes: Imports + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + 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: thomas.pedersen@rstudio.com + 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: '2022' + url: https://CRAN.R-project.org/package=ggplot2 +- type: software + title: Hmisc + abstract: 'Hmisc: Harrell Miscellaneous' + notes: Imports + authors: + - family-names: Harrell Jr + given-names: Frank E + email: fh@fharrell.com + orcid: https://orcid.org/0000-0002-8271-5493 + year: '2022' + url: https://CRAN.R-project.org/package=Hmisc +- type: software + title: methods + 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: rlang + abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features' + notes: Imports + authors: + - family-names: Henry + given-names: Lionel + email: lionel@rstudio.com + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + year: '2022' + url: https://CRAN.R-project.org/package=rlang +- type: software + title: stats + 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: utils + 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: covr + abstract: 'covr: Test Coverage for Packages' + notes: Suggests + authors: + - family-names: Hester + given-names: Jim + email: james.f.hester@gmail.com + year: '2022' + url: https://CRAN.R-project.org/package=covr +- type: software + title: folio + abstract: 'folio: Datasets for Teaching Archaeology and Paleontology' + notes: Suggests + authors: + - family-names: Frerebeau + given-names: Nicolas + email: nicolas.frerebeau@u-bordeaux-montaigne.fr + orcid: https://orcid.org/0000-0001-5759-4944 + year: '2022' + url: https://CRAN.R-project.org/package=folio +- type: software + title: knitr + abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R' + notes: Suggests + authors: + - family-names: Xie + given-names: Yihui + email: xie@yihui.name + orcid: https://orcid.org/0000-0003-0645-5666 + year: '2022' + url: https://CRAN.R-project.org/package=knitr +- type: software + title: rmarkdown + abstract: 'rmarkdown: Dynamic Documents for R' + notes: Suggests + authors: + - family-names: Allaire + given-names: JJ + email: jj@rstudio.com + - family-names: Xie + given-names: Yihui + email: xie@yihui.name + orcid: https://orcid.org/0000-0003-0645-5666 + - family-names: McPherson + given-names: Jonathan + email: jonathan@rstudio.com + - family-names: Luraschi + given-names: Javier + email: javier@rstudio.com + - family-names: Ushey + given-names: Kevin + email: kevin@rstudio.com + - family-names: Atkins + given-names: Aron + email: aron@rstudio.com + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + - family-names: Cheng + given-names: Joe + email: joe@rstudio.com + - family-names: Chang + given-names: Winston + email: winston@rstudio.com + - family-names: Iannone + given-names: Richard + email: rich@rstudio.com + orcid: https://orcid.org/0000-0003-3925-190X + year: '2022' + url: https://CRAN.R-project.org/package=rmarkdown +- type: software + title: testthat + abstract: 'testthat: Unit Testing for R' + notes: Suggests + authors: + - family-names: Wickham + given-names: Hadley + email: hadley@rstudio.com + year: '2022' + url: https://CRAN.R-project.org/package=testthat + version: '>= 3.0.0' +- type: software + title: vdiffr + abstract: 'vdiffr: Visual Regression Testing and Graphical Diffing' + notes: Suggests + authors: + - family-names: Henry + given-names: Lionel + email: lionel@rstudio.com + - family-names: Pedersen + given-names: Thomas Lin + email: thomas.pedersen@rstudio.com + orcid: https://orcid.org/0000-0002-5147-4711 + - family-names: Luciani + given-names: T Jake + email: jake@apache.org + - family-names: Decorde + given-names: Matthieu + email: matthieu.decorde@ens-lyon.fr + - family-names: Lise + given-names: Vaudor + email: lise.vaudor@ens-lyon.fr + year: '2022' + url: https://CRAN.R-project.org/package=vdiffr + version: '>= 1.0.0' identifiers: - description: The concept DOI. type: doi diff --git a/DESCRIPTION b/DESCRIPTION index 2c02ece..419334a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: kairos Title: Analysis of Chronological Patterns from Archaeological Count Data -Version: 1.0.0.9000 +Version: 1.0.1 Authors@R: c(person(given = "Nicolas", family = "Frerebeau", diff --git a/NEWS.md b/NEWS.md index c7c9fa7..6cfbd91 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,5 @@ -# kairos 1.0.0.9000 +# kairos 1.0.1 + ## Bugfixes & changes * Fix aoristic sum calculation (#1). `aoristic()` now calculates weights within the time blocks rather than at the break dates between blocks. diff --git a/R/kairos-package.R b/R/kairos-package.R index 1817365..6264a2f 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 1.0.0 \cr +#' **Version:** \tab 1.0.1 \cr #' **License:** \tab GPL-3 \cr #' } #' diff --git a/codemeta.json b/codemeta.json index 0b614f3..6249414 100644 --- a/codemeta.json +++ b/codemeta.json @@ -11,13 +11,13 @@ "relatedLink": "https://packages.tesselle.org/kairos/", "issueTracker": "https://github.com/tesselle/kairos/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "1.0.0", + "version": "1.0.1", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.1.1 (2021-08-10)", + "runtimePlatform": "R version 4.1.2 (2021-11-01)", "author": [ { "@type": "Person", @@ -194,6 +194,18 @@ }, "sameAs": "https://CRAN.R-project.org/package=ggplot2" }, + { + "@type": "SoftwareApplication", + "identifier": "Hmisc", + "name": "Hmisc", + "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=Hmisc" + }, { "@type": "SoftwareApplication", "identifier": "methods", @@ -222,10 +234,10 @@ "name": "utils" } ], - "fileSize": "1452.929KB", - "contIntegration": "https://codecov.io/gh/tesselle/kairos", + "fileSize": "816.398KB", + "contIntegration": "https://app.codecov.io/gh/tesselle/kairos", "developmentStatus": "https://www.repostatus.org/#active", - "readme": "https://github.com/tesselle/kairos/blob/master/README.md", + "readme": "https://github.com/tesselle/kairos/blob/main/README.md", "keywords": [ "r-package", "archaeology", @@ -236,7 +248,7 @@ "citation": [ { "@type": "SoftwareSourceCode", - "datePublished": "2021", + "datePublished": "2022", "author": [ { "@type": "Person", @@ -245,8 +257,11 @@ } ], "name": "kairos: Analysis of Chronological Patterns from Archaeological Count Data", - "url": "https://packages.tesselle.org/kairos", - "description": "R package version 1.0.0" + "identifier": "10.5281/zenodo.5653896", + "url": "https://packages.tesselle.org/kairos/", + "description": "R package version 1.0.1", + "@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 1edf428..abdc13b 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +1,5 @@ ## Test environments -* Local R installation: R 4.1.1 +* Local R installation: R 4.1.2 * Ubuntu 20.04 (on GitHub Actions): R devel, release, oldrel * Windows (on GitHub Actions and win-builder): R devel, release, oldrel * MacOS (on GitHub Actions): R release @@ -8,4 +8,5 @@ 0 errors | 0 warnings | 1 note -* This is a new release. +* CRAN package check warning caused by default.stringsAsFactors() has been fixed. +* Some links in the documentation point to articles behind paywalls that may return an error. diff --git a/inst/CITATION b/inst/CITATION index 336e908..7f22264 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -4,17 +4,17 @@ citEntry( entry = "Manual", title = "kairos: Analysis of Chronological Patterns from Archaeological Count Data", author = c(person("Nicolas", "Frerebeau", role = "aut")), - year = "2021", + year = "2022", organization = "Université Bordeaux Montaigne", address = "Pessac, France", - note = "R package version 1.0.0", + note = "R package version 1.0.1", url = "https://packages.tesselle.org/kairos/", doi = "10.5281/zenodo.5653896", textVersion = - paste("Frerebeau, Nicolas (2021).", + paste("Frerebeau, Nicolas (2022).", "kairos: Analysis of Chronological Patterns from Archaeological Count Data.", - "R package version 1.0.0", + "R package version 1.0.1", "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 de4d563..9ff472a 100644 --- a/man/kairos-package.Rd +++ b/man/kairos-package.Rd @@ -15,7 +15,7 @@ A toolkit for absolute dating and analysis of chronological patterns. This packa \tabular{ll}{ \strong{Package:} \tab kairos \cr \strong{Type:} \tab Package \cr -\strong{Version:} \tab 1.0.0 \cr +\strong{Version:} \tab 1.0.1 \cr \strong{License:} \tab GPL-3 \cr } }