Prepare for next release

.gitattributes

@@ -0,0 +1,6 @@
+/.github export-ignore
+.gitattributes export-ignore
+.gitignore export-ignore
+
+_pkgdown.yml export-ignore
+codecov.yml export-ignore

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: [email protected]
     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: [email protected]
     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: [email protected]
+  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: [email protected]
+    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: [email protected]
+  - family-names: Xie
+    given-names: Yihui
+    email: [email protected]
+    orcid: https://orcid.org/0000-0003-0645-5666
+  - family-names: McPherson
+    given-names: Jonathan
+    email: [email protected]
+  - family-names: Luraschi
+    given-names: Javier
+    email: [email protected]
+  - family-names: Ushey
+    given-names: Kevin
+    email: [email protected]
+  - family-names: Atkins
+    given-names: Aron
+    email: [email protected]
+  - family-names: Wickham
+    given-names: Hadley
+    email: [email protected]
+  - family-names: Cheng
+    given-names: Joe
+    email: [email protected]
+  - family-names: Chang
+    given-names: Winston
+    email: [email protected]
+  - family-names: Iannone
+    given-names: Richard
+    email: [email protected]
+    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: [email protected]
+  year: '2022'
+  url: https://CRAN.R-project.org/package=testthat
+  version: '>= 3.0.0'
 identifiers:
 - description: The concept DOI.
   type: doi

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",

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

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
 #'  }

README.Rmd

@@ -1,7 +1,5 @@
 ---
 output: github_document
-editor_options: 
-  chunk_output_type: console
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -19,13 +17,13 @@ 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://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)
 

README.md

@@ -6,16 +6,23 @@
 <!-- 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://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)
+<a href="https://tesselle.r-universe.dev" class="pkgdown-devel"><img
+src="https://tesselle.r-universe.dev/badges/arkhe"
+alt="r-universe" /></a>
+<a href="https://cran.r-project.org/package=arkhe"
+class="pkgdown-release"><img
+src="http://www.r-pkg.org/badges/version/arkhe"
+alt="CRAN Version" /></a>
+<a href="https://cran.r-project.org/web/checks/check_results_arkhe.html"
+class="pkgdown-release"><img
+src="https://cranchecks.info/badges/worst/arkhe"
+alt="CRAN checks" /></a>
+<a href="https://cran.r-project.org/package=arkhe"
+class="pkgdown-release"><img
+src="http://cranlogs.r-pkg.org/badges/arkhe" alt="CRAN Downloads" /></a>
 
 [![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)
 #> <AbundanceSummary: 15 x 5>
 #> 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)
 #> --------------------------------------------------------------------------------
 ```
 

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"
     }

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