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 8f8066b..07b05f9 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,5 @@ # ----------------------------------------------------------- -# CITATION file created with {cffr} R package, v0.3.0 +# CITATION file created with {cffr} R package, v0.5.0 # See also: https://docs.ropensci.org/cffr/ # ----------------------------------------------------------- @@ -8,7 +8,7 @@ message: 'To cite package "arkhe" in publications use:' type: software license: GPL-3.0-or-later title: 'arkhe: Tools for Cleaning Rectangular Data' -version: 1.1.0 +version: 1.2.0 doi: 10.5281/zenodo.3526659 abstract: A dependency-free collection of simple functions for cleaning rectangular data. This package allows to detect, count and replace values or discard rows/columns @@ -32,7 +32,7 @@ preferred-citation: year: '2023' location: name: Pessac, France - notes: R package version 1.1.0 + notes: R package version 1.2.0 url: https://packages.tesselle.org/arkhe/ doi: 10.5281/zenodo.3526659 institution: @@ -48,19 +48,18 @@ contact: affiliation: Université Bordeaux Montaigne keywords: - data cleaning -- archaeology -- archaeological science +- statistics - r package references: - type: software title: 'R: A Language and Environment for Statistical Computing' notes: Depends + url: https://www.R-project.org/ authors: - name: R Core Team location: name: Vienna, Austria year: '2023' - url: https://www.R-project.org/ institution: name: R Foundation for Statistical Computing version: '>= 3.3' @@ -73,7 +72,6 @@ references: location: name: Vienna, Austria year: '2023' - url: https://www.R-project.org/ institution: name: R Foundation for Statistical Computing - type: software @@ -85,7 +83,6 @@ references: location: name: Vienna, Austria year: '2023' - url: https://www.R-project.org/ institution: name: R Foundation for Statistical Computing - type: software @@ -97,19 +94,19 @@ references: location: name: Vienna, Austria year: '2023' - url: https://www.R-project.org/ institution: name: R Foundation for Statistical Computing - type: software title: testthat abstract: 'testthat: Unit Testing for R' notes: Suggests + url: https://testthat.r-lib.org + repository: https://CRAN.R-project.org/package=testthat authors: - family-names: Wickham given-names: Hadley email: hadley@rstudio.com year: '2023' - url: https://CRAN.R-project.org/package=testthat version: '>= 3.0.0' identifiers: - description: The concept DOI. diff --git a/DESCRIPTION b/DESCRIPTION index 42074f9..4c6061c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: arkhe Title: Tools for Cleaning Rectangular Data -Version: 1.1.0.9000 +Version: 1.2.0 Authors@R: c(person(given = "Nicolas", family = "Frerebeau", @@ -34,7 +34,7 @@ Suggests: testthat (>= 3.0.0) Config/testthat/edition: 3 Encoding: UTF-8 -RoxygenNote: 7.2.1 +RoxygenNote: 7.2.3 Roxygen: list(markdown = TRUE) Collate: 'AllGenerics.R' diff --git a/NEWS.md b/NEWS.md index 10ba254..7f7e040 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# arkhe 1.1.0.9000 +# arkhe 1.2.0 ## New classes and methods * Add `math_lcm()` and `math_gcd()` to compute the lowest common multiple and the greatest common divisor. * Add `interval_hdr()` and `interval_credible()` to compute the credible intervals. diff --git a/R/arkhe-package.R b/R/arkhe-package.R index 4c485de..4a678fb 100644 --- a/R/arkhe-package.R +++ b/R/arkhe-package.R @@ -2,7 +2,7 @@ #' \tabular{ll}{ #' **Package:** \tab arkhe \cr #' **Type:** \tab Package \cr -#' **Version:** \tab 1.1.0 \cr +#' **Version:** \tab 1.2.0 \cr #' **License:** \tab GPL-3 \cr #' **Zenodo:** \tab \doi{10.5281/zenodo.3526659} \cr #' } diff --git a/README.Rmd b/README.Rmd index b096b7f..e416c56 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,7 +17,7 @@ knitr::opts_chunk$set( [![R-CMD-check](https://github.com/tesselle/arkhe/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/arkhe/actions) -[![codecov](https://codecov.io/gh/tesselle/arkhe/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tesselle/arkhe) +[![codecov](https://codecov.io/gh/tesselle/arkhe/branch/main/graph/badge.svg?token=3TUSMmF18Q)](https://app.codecov.io/gh/tesselle/arkhe) [![CodeFactor](https://www.codefactor.io/repository/github/tesselle/arkhe/badge/main)](https://www.codefactor.io/repository/github/tesselle/arkhe/overview/main) [![Dependencies](https://tinyverse.netlify.com/badge/arkhe)](https://cran.r-project.org/package=arkhe) diff --git a/README.md b/README.md index 64fcf2f..e746882 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![R-CMD-check](https://github.com/tesselle/arkhe/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/arkhe/actions) -[![codecov](https://codecov.io/gh/tesselle/arkhe/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tesselle/arkhe) +[![codecov](https://codecov.io/gh/tesselle/arkhe/branch/main/graph/badge.svg?token=3TUSMmF18Q)](https://app.codecov.io/gh/tesselle/arkhe) [![CodeFactor](https://www.codefactor.io/repository/github/tesselle/arkhe/badge/main)](https://www.codefactor.io/repository/github/tesselle/arkhe/overview/main) [![Dependencies](https://tinyverse.netlify.com/badge/arkhe)](https://cran.r-project.org/package=arkhe) @@ -70,49 +70,49 @@ k <- sample(1:25, 3, FALSE) X[k] <- NA X #> [,1] [,2] [,3] [,4] [,5] -#> [1,] 4 6 1 2 8 -#> [2,] 6 8 2 7 10 -#> [3,] NA 1 2 9 2 -#> [4,] NA 9 NA 10 8 -#> [5,] 5 4 3 6 6 +#> [1,] 2 5 NA 6 NA +#> [2,] 4 1 5 2 5 +#> [3,] 2 6 NA 6 10 +#> [4,] 1 7 6 5 6 +#> [5,] 6 1 8 8 6 ## Count missing values in rows count(X, f = is.na, margin = 1) -#> [1] 0 0 1 2 0 +#> [1] 2 0 1 0 0 ## Count non-missing values in columns count(X, f = is.na, margin = 2, negate = TRUE) -#> [1] 3 5 4 5 5 +#> [1] 5 5 3 5 4 ## Find row with NA detect(X, f = is.na, margin = 1) -#> [1] FALSE FALSE TRUE TRUE FALSE +#> [1] TRUE FALSE TRUE FALSE FALSE ## Find column without any NA detect(X, f = is.na, margin = 2, negate = TRUE, all = TRUE) -#> [1] FALSE TRUE FALSE TRUE TRUE +#> [1] TRUE TRUE FALSE TRUE FALSE ## Remove row with any NA discard(X, f = is.na, margin = 1, all = FALSE) #> [,1] [,2] [,3] [,4] [,5] -#> [1,] 4 6 1 2 8 -#> [2,] 6 8 2 7 10 -#> [3,] 5 4 3 6 6 +#> [1,] 4 1 5 2 5 +#> [2,] 1 7 6 5 6 +#> [3,] 6 1 8 8 6 ## Remove column with any NA discard(X, f = is.na, margin = 2, all = FALSE) #> [,1] [,2] [,3] -#> [1,] 6 2 8 -#> [2,] 8 7 10 -#> [3,] 1 9 2 -#> [4,] 9 10 8 -#> [5,] 4 6 6 +#> [1,] 2 5 6 +#> [2,] 4 1 2 +#> [3,] 2 6 6 +#> [4,] 1 7 5 +#> [5,] 6 1 8 ## Replace NA with zeros replace_NA(X, value = 0) #> [,1] [,2] [,3] [,4] [,5] -#> [1,] 4 6 1 2 8 -#> [2,] 6 8 2 7 10 -#> [3,] 0 1 2 9 2 -#> [4,] 0 9 0 10 8 -#> [5,] 5 4 3 6 6 +#> [1,] 2 5 0 6 0 +#> [2,] 4 1 5 2 5 +#> [3,] 2 6 0 6 10 +#> [4,] 1 7 6 5 6 +#> [5,] 6 1 8 8 6 ``` ## Contributing diff --git a/codemeta.json b/codemeta.json index 587f1ef..1213a28 100644 --- a/codemeta.json +++ b/codemeta.json @@ -8,13 +8,13 @@ "codeRepository": "https://github.com/tesselle/arkhe", "issueTracker": "https://github.com/tesselle/arkhe/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 4.2.2 Patched (2022-11-10 r83330)", + "runtimePlatform": "R version 4.3.0 (2023-04-21)", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -87,7 +87,7 @@ }, "SystemRequirements": null }, - "fileSize": "230.734KB", + "fileSize": "247.115KB", "citation": [ { "@type": "SoftwareSourceCode", @@ -99,10 +99,10 @@ "familyName": "Frerebeau" } ], - "name": "arkhe: Tools for Cleaning Rectangular Data", + "name": "{arkhe: Tools for Cleaning Rectangular Data}", "identifier": "10.5281/zenodo.3526659", "url": "https://packages.tesselle.org/arkhe/", - "description": "R package version 1.1.0", + "description": "R package version 1.2.0", "@id": "https://doi.org/10.5281/zenodo.3526659", "sameAs": "https://doi.org/10.5281/zenodo.3526659" } @@ -111,5 +111,5 @@ "readme": "https://github.com/tesselle/arkhe/blob/main/README.md", "contIntegration": ["https://github.com/tesselle/arkhe/actions", "https://app.codecov.io/gh/tesselle/arkhe"], "developmentStatus": "https://www.repostatus.org/#active", - "keywords": ["archaeology", "archaeological-science", "r-package", "data-cleaning"] + "keywords": ["r-package", "data-cleaning", "statistics"] } diff --git a/cran-comments.md b/cran-comments.md index fd7f17c..d798696 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +1,5 @@ ## Test environments -* Local R installation: R 4.2.2 +* Local R installation: R 4.3.0 * 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/inst/CITATION b/inst/CITATION index 9f3202b..62fdff3 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,21 +1,13 @@ -citHeader("To cite arkhe in publications use:") - -citEntry( - entry = "Manual", - title = "arkhe: Tools for Cleaning Rectangular Data", - author = c(person("Nicolas", "Frerebeau", role = "aut")), +bibentry( + bibtype = "Manual", + header = "To cite arkhe in publications use:", + footer = "This package is a part of the tesselle project .", + author = "Nicolas Frerebeau", + title = "{arkhe: Tools for Cleaning Rectangular Data}", year = "2023", 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/arkhe/", - doi = "10.5281/zenodo.3526659", - - textVersion = - paste("Frerebeau, Nicolas (2023).", - "arkhe: Tools for Cleaning Rectangular Data.", - "R package version 1.1.0", - "Université Bordeaux Montaigne, Pessac, France.", - "DOI 10.5281/zenodo.3526659.", - "URL https://packages.tesselle.org/arkhe.") + doi = "10.5281/zenodo.3526659" ) diff --git a/man/arkhe-package.Rd b/man/arkhe-package.Rd index 2d69614..ec22d5e 100644 --- a/man/arkhe-package.Rd +++ b/man/arkhe-package.Rd @@ -15,7 +15,7 @@ A dependency-free collection of simple functions for cleaning rectangular data. \tabular{ll}{ \strong{Package:} \tab arkhe \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 \strong{Zenodo:} \tab \doi{10.5281/zenodo.3526659} \cr } diff --git a/revdep/README.md b/revdep/README.md index 54c9aa5..49e0b84 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -2,23 +2,23 @@ |field |value | |:--------|:-----------------------------------------------------------------------------| -|version |R version 4.2.2 Patched (2022-11-10 r83330) | -|os |Ubuntu 20.04.5 LTS | +|version |R version 4.3.0 (2023-04-21) | +|os |Ubuntu 20.04.6 LTS | |system |x86_64, linux-gnu | |ui |RStudio | |language |(EN) | |collate |fr_FR.UTF-8 | |ctype |fr_FR.UTF-8 | |tz |Europe/Paris | -|date |2023-01-06 | -|rstudio |2022.12.0+353 Elsbeth Geranium (desktop) | +|date |2023-05-10 | +|rstudio |2023.03.0+386 Cherry Blossom (desktop) | |pandoc |2.19.2 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) | # Dependencies |package |old |new |Δ | |:-------|:-----|:-----|:--| -|arkhe |1.0.0 |1.1.0 |* | +|arkhe |1.1.0 |1.2.0 |* | # Revdeps