Prepare for next release

tesselle · May 10, 2023 · d4e188d · d4e188d
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diff --git 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 <https://documentation.tesselle.org>.
+* 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 <https://www.tesselle.org/style.html>.
 
 ### 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![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
@@ -6,7 +6,7 @@
 <!-- badges: start -->
 
 [![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
@@ -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
@@ -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
@@ -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 <https://www.tesselle.org>.",
+  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
diff --git 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