diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..ff3ca24 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,6 @@ +/.github export-ignore +.gitattributes export-ignore +.gitignore export-ignore + +_pkgdown.yml export-ignore +codecov.yml export-ignore diff --git a/CITATION.cff b/CITATION.cff index 75882cc..66255a1 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, v0.2.2 # 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: Representation of Archaeological Data' -version: 0.4.0.9000 +version: 0.5.0 abstract: A collection of classes that represent archaeological data. This package provides a set of S4 classes that represent different special types of matrix (absolute/relative frequency, presence/absence data, co-occurrence matrix, etc.) upon which package @@ -31,7 +31,7 @@ preferred-citation: email: nicolas.frerebeau@u-bordeaux-montaigne.fr orcid: https://orcid.org/0000-0001-5759-4944 affiliation: Université Bordeaux Montaigne - version: 0.4.0.9000 + version: 0.5.0 abstract: A collection of classes that represent archaeological data. This package provides a set of S4 classes that represent different special types of matrix (absolute/relative frequency, presence/absence data, co-occurrence matrix, etc.) @@ -48,8 +48,13 @@ 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 + - data-representation + - r-package license: GPL-3.0-or-later - year: '2021' + year: '2022' repository: https://CRAN.R-project.org/package=arkhe repository-code: https://github.com/tesselle/arkhe url: https://packages.tesselle.org/arkhe/ @@ -64,6 +69,126 @@ 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: '>= 3.3' +- 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: 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: 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' identifiers: - description: The concept DOI. type: doi diff --git a/DESCRIPTION b/DESCRIPTION index 89062dc..b59ae3e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: arkhe Title: Representation of Archaeological Data -Version: 0.4.0.9000 +Version: 0.5.0 Authors@R: c(person(given = "Nicolas", family = "Frerebeau", diff --git a/NEWS.md b/NEWS.md index acb2a51..a4ae576 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,11 +1,12 @@ -# arkhe 0.4.0.9000 +# arkhe 0.5.0 ## New classes and methods * Add `assign_rownames()` and `assign_colnames()` to make a specific row/column the column/row names of a `data.frame`. +* Add `assert_count()` to validate count data (absolute frequencies/integer). * Add `count()` to count values by rows/columns according to a given predicate. * Add `detect()` to find rows/columns in an array-like object according to a given predicate. * Add `compact()` to remove rows/columns in an array-like object according to a given predicate. -* Add `resample()` to sample observations from a multinomial distribution (partial bootstrap). * Add `jackknife()` for jackknife estimation. +* Add `confidence()` to compute confidence interval for the mean. # arkhe 0.4.0 ## New classes and methods diff --git a/R/arkhe-package.R b/R/arkhe-package.R index 084ce5a..9e7f01f 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 0.4.0 \cr +#' **Version:** \tab 0.5.0 \cr #' **License:** \tab GPL-3 \cr #' **Zenodo:** \tab \doi{10.5281/zenodo.3526659} \cr #' } diff --git a/README.Rmd b/README.Rmd index 2582327..40ccb68 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,7 +1,5 @@ --- output: github_document -editor_options: - chunk_output_type: console --- @@ -19,13 +17,13 @@ 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://codecov.io/gh/tesselle/arkhe) +[![codecov](https://codecov.io/gh/tesselle/arkhe/branch/main/graph/badge.svg)](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) -[![r-universe](https://tesselle.r-universe.dev/badges/arkhe)](https://tesselle.r-universe.dev) -[![CRAN Version](http://www.r-pkg.org/badges/version/arkhe)](https://cran.r-project.org/package=arkhe) -[![CRAN checks](https://cranchecks.info/badges/worst/arkhe)](https://cran.r-project.org/web/checks/check_results_arkhe.html) -[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/arkhe)](https://cran.r-project.org/package=arkhe) +[![r-universe](https://tesselle.r-universe.dev/badges/arkhe)](https://tesselle.r-universe.dev){.pkgdown-devel} +[![CRAN Version](http://www.r-pkg.org/badges/version/arkhe)](https://cran.r-project.org/package=arkhe){.pkgdown-release} +[![CRAN checks](https://cranchecks.info/badges/worst/arkhe)](https://cran.r-project.org/web/checks/check_results_arkhe.html){.pkgdown-release} +[![CRAN Downloads](http://cranlogs.r-pkg.org/badges/arkhe)](https://cran.r-project.org/package=arkhe){.pkgdown-release} [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) diff --git a/README.md b/README.md index 78850a9..98f269b 100644 --- a/README.md +++ b/README.md @@ -6,16 +6,23 @@ [![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://codecov.io/gh/tesselle/arkhe) +[![codecov](https://codecov.io/gh/tesselle/arkhe/branch/main/graph/badge.svg)](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) -[![r-universe](https://tesselle.r-universe.dev/badges/arkhe)](https://tesselle.r-universe.dev) -[![CRAN -Version](http://www.r-pkg.org/badges/version/arkhe)](https://cran.r-project.org/package=arkhe) -[![CRAN -checks](https://cranchecks.info/badges/worst/arkhe)](https://cran.r-project.org/web/checks/check_results_arkhe.html) -[![CRAN -Downloads](http://cranlogs.r-pkg.org/badges/arkhe)](https://cran.r-project.org/package=arkhe) + + + +CRAN Downloads [![Project Status: Active – The project has reached a stable, usable state and is being actively @@ -147,63 +154,63 @@ Z <- as_count(Y) ## Get groups get_samples(Z) -#> [1] "b" "e" "a" "c" "b" "b" "d" "d" "a" "a" "d" "c" "c" "c" "e" +#> [1] "d" "a" "b" "e" "b" "e" "b" "d" "e" "d" "d" "e" "e" "e" "a" ## Get groups get_groups(Z) -#> [1] "A" "E" "D" "B" "A" "B" "B" "B" "D" "C" "D" "A" "E" "B" "A" +#> [1] "A" "E" "A" "B" "A" "D" "A" "E" "D" "B" "E" "D" "A" "A" "C" ## Get dates get_dates(Z) -#> [1] 1447 1441 1423 1411 1408 1425 1435 1415 1443 1416 1416 1442 1442 1451 1437 +#> [1] 1442 1449 1431 1439 1429 1411 1400 1439 1437 1440 1444 1418 1450 1436 1427 ## Get chronology get_terminus(Z) #> tpq taq -#> row1 1318 1471 -#> row2 1374 1483 -#> row3 1394 1470 -#> row4 1385 1465 -#> row5 1399 1452 -#> row6 1339 1471 -#> row7 1317 1455 -#> row8 1368 1495 -#> row9 1343 1465 -#> row10 1332 1455 -#> row11 1343 1483 -#> row12 1392 1490 -#> row13 1324 1478 -#> row14 1364 1477 -#> row15 1356 1466 +#> row1 1302 1486 +#> row2 1346 1496 +#> row3 1349 1456 +#> row4 1372 1485 +#> row5 1370 1495 +#> row6 1318 1455 +#> row7 1389 1467 +#> row8 1377 1488 +#> row9 1346 1462 +#> row10 1308 1487 +#> row11 1362 1464 +#> row12 1400 1451 +#> row13 1312 1464 +#> row14 1316 1483 +#> row15 1332 1468 ## Summarize summary(Z) #> #> A ------------------------------------------------------------------------------ -#> * Observations: 4 +#> * Observations: 6 #> * Variables: 5 #> * Replicated measurements: TRUE -#> * Chronology: 1318 - 1490 (year CE) +#> * Chronology: 1302 - 1495 (year CE) #> B ------------------------------------------------------------------------------ -#> * Observations: 5 +#> * Observations: 2 #> * Variables: 5 -#> * Replicated measurements: TRUE -#> * Chronology: 1317 - 1495 (year CE) +#> * Replicated measurements: FALSE +#> * Chronology: 1308 - 1487 (year CE) #> C ------------------------------------------------------------------------------ #> * Observation: 1 #> * Variables: 5 #> * Replicated measurements: FALSE -#> * Chronology: 1332 - 1455 (year CE) +#> * Chronology: 1332 - 1468 (year CE) #> D ------------------------------------------------------------------------------ #> * Observations: 3 #> * Variables: 5 #> * Replicated measurements: TRUE -#> * Chronology: 1343 - 1483 (year CE) +#> * Chronology: 1318 - 1462 (year CE) #> E ------------------------------------------------------------------------------ -#> * Observations: 2 +#> * Observations: 3 #> * Variables: 5 -#> * Replicated measurements: FALSE -#> * Chronology: 1324 - 1483 (year CE) +#> * Replicated measurements: TRUE +#> * Chronology: 1346 - 1496 (year CE) #> -------------------------------------------------------------------------------- ``` diff --git a/codemeta.json b/codemeta.json index fe22a8f..66b6230 100644 --- a/codemeta.json +++ b/codemeta.json @@ -8,7 +8,7 @@ "codeRepository": "https://github.com/tesselle/arkhe", "issueTracker": "https://github.com/tesselle/arkhe/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "0.4.0.9000", + "version": "0.5.0", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -123,7 +123,7 @@ }, "SystemRequirements": null }, - "fileSize": "970.177KB", + "fileSize": "970.161KB", "citation": [ { "@type": "SoftwareSourceCode", @@ -138,7 +138,7 @@ "name": "arkhe: Representation of Archaeological Data", "identifier": "10.5281/zenodo.3526659", "url": "https://packages.tesselle.org/arkhe/", - "description": "R package version 0.4.0", + "description": "R package version 0.5.0", "@id": "https://doi.org/10.5281/zenodo.3526659", "sameAs": "https://doi.org/10.5281/zenodo.3526659" } diff --git a/cran-comments.md b/cran-comments.md index 91b8132..e269e68 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 4.2.0 * 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 @@ -10,7 +10,7 @@ ## Reverse dependencies -We checked 1 reverse dependency, comparing R CMD check results across CRAN and dev versions of this package. +We checked 3 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. * We saw 0 new problems * We failed to check 0 packages diff --git a/inst/CITATION b/inst/CITATION index 9625260..f2881f2 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -7,14 +7,14 @@ citEntry( year = "2021", organization = "Université Bordeaux Montaigne", address = "Pessac, France", - note = "R package version 0.4.0", + note = "R package version 0.5.0", url = "https://packages.tesselle.org/arkhe/", doi = "10.5281/zenodo.3526659", textVersion = paste("Frerebeau, Nicolas (2021).", "arkhe: Representation of Archaeological Data.", - "R package version 0.4.0", + "R package version 0.5.0", "Université Bordeaux Montaigne, Pessac, France.", "DOI 10.5281/zenodo.3526659.", "URL https://packages.tesselle.org/arkhe.") diff --git a/man/arkhe-package.Rd b/man/arkhe-package.Rd index 759b236..eb6a66d 100644 --- a/man/arkhe-package.Rd +++ b/man/arkhe-package.Rd @@ -15,7 +15,7 @@ A collection of classes that represent archaeological data. This package provide \tabular{ll}{ \strong{Package:} \tab arkhe \cr \strong{Type:} \tab Package \cr -\strong{Version:} \tab 0.4.0 \cr +\strong{Version:} \tab 0.5.0 \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 460532f..dc5d560 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,22 +1,24 @@ # Platform -|field |value | -|:--------|:----------------------------| -|version |R version 4.1.1 (2021-08-10) | -|os |Ubuntu 20.04.3 LTS | -|system |x86_64, linux-gnu | -|ui |RStudio | -|language |(EN) | -|collate |fr_FR.UTF-8 | -|ctype |fr_FR.UTF-8 | -|tz |Europe/Paris | -|date |2021-09-18 | +|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 |2022-06-12 | +|rstudio |2022.02.3+492 Prairie Trillium (desktop) | +|pandoc |2.17.1.1 @ /usr/lib/rstudio/bin/quarto/bin/ (via rmarkdown) | # Dependencies |package |old |new |Δ | |:-------|:-----|:-----|:--| -|arkhe |0.3.1 |0.4.0 |* | +|arkhe |0.4.0 |0.5.0 |* | # Revdeps diff --git a/revdep/cran.md b/revdep/cran.md index 782ef68..29c1961 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,6 +1,6 @@ ## revdepcheck results -We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 3 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. * We saw 0 new problems * We failed to check 0 packages