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)
+
+
+
+
[![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