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tesselle · May 16, 2024 · 76b5e8a · 76b5e8a
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diff --git a/CITATION.cff b/CITATION.cff
@@ -1,5 +1,5 @@
 # -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v0.5.0
+# CITATION file created with {cffr} R package, v1.0.0
 # See also: https://docs.ropensci.org/cffr/
 # -----------------------------------------------------------
 
@@ -8,7 +8,7 @@ message: 'To cite package "tabula" in publications use:'
 type: software
 license: GPL-3.0-or-later
 title: 'tabula: Analysis and Visualization of Archaeological Count Data'
-version: 3.0.1
+version: 3.1.0
 doi: 10.21105/joss.01821
 abstract: 'An easy way to examine archaeological count data. This package provides
   several tests and measures of diversity: heterogeneity and evenness (Brillouin,
@@ -68,14 +68,13 @@ references:
   authors:
   - family-names: Frerebeau
     given-names: Nicolas
-  year: '2023'
-  location:
-    name: Pessac, France
-  notes: R package version 3.0.1
-  url: https://packages.tesselle.org/tabula/
-  doi: 10.5281/zenodo.1489944
+  year: '2024'
   institution:
     name: Université Bordeaux Montaigne
+    address: Pessac, France
+  notes: R package version 3.1.0
+  url: https://packages.tesselle.org/tabula/
+  doi: 10.5281/zenodo.1489944
 identifiers:
 - description: The concept DOI.
   type: doi
@@ -127,4 +126,4 @@ identifiers:
   value: 10.5281/zenodo.10214364
 - description: The Software Heritage identifier for version 2.0.0.
   type: swh
-  value: swh:1:dir:1ea4b50f6ac77dac3591b9156780b647528e1452
+  value: swh:1:rel:7a252fd4e6b5c8650fcf135c8c4627366cd04d37
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,11 @@
 Package: tabula
 Title: Analysis and Visualization of Archaeological Count Data
-Version: 3.0.1.9000
+Version: 3.1.0
 Authors@R: c(
     person("Nicolas", "Frerebeau", , "nicolas.frerebeau@u-bordeaux-montaigne.fr", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-5759-4944", affiliation = "Université Bordeaux Montaigne")),
     person("Brice", "Lebrun", , "brice.lebrun@u-bordeaux-montaigne.fr", role = "ctb",
-           comment = c(ORCID = "0000-0001-7503-8685", affiliation = "Université Bordeaux Montaigne")),
+           comment = c(ORCID = "0000-0001-7503-8685", "Logo designer")),
     person("Matthew", "Peeples", , "matthew.peeples@asu.edu", role = "ctb",
            comment = c(ORCID = "0000-0003-4496-623X", affiliation = "Arizona State University")),
     person("Ben", "Marwick", , "bmarwick@uw.edu", role = "ctb",
@@ -52,7 +52,7 @@ VignetteBuilder:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Collate: 
     'AllClasses.R'
     'AllGenerics.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,17 @@
-# tabula 3.0.1.9000
+# tabula 3.1.0
+## New classes and methods
+* Add `she()` to plot SHE analysis.
+* Add `profiles()` to plot diversity profiles.
+* Add `test_shannon()` and `test_simpson()` to compare the Shannon and Simpson diversities in two samples.
+* Add `index_squares()` to compute Alroy (2018) richness estimator.
+
 ## Enhancements
 * `plot_heatmap()` gained a new argument to use a fixed aspect ratio.
-* Improve gradient legend.
+* Improve color gradient in plot legends.
 
-## Internals
-* Use **graffiti**.
+## Bugfixes & changes
+* Fix ACE species richness estimator.
+* Deprecate `test_diversity()`.
 
 # tabula 3.0.1
 ## Enhancements

diff --git a/R/tabula-package.R b/R/tabula-package.R
@@ -2,7 +2,7 @@
 #' \tabular{ll}{
 #'  **Package:** \tab tabula \cr
 #'  **Type:** \tab Package \cr
-#'  **Version:** \tab 3.0.1 \cr
+#'  **Version:** \tab 3.1.0 \cr
 #'  **License:** \tab GPL-3 \cr
 #'  **Zenodo:** \tab \doi{10.5281/zenodo.1489944} \cr
 #'  **JOSS:** \tab \doi{10.21105/joss.01821} \cr

diff --git a/README.Rmd b/README.Rmd
@@ -21,7 +21,7 @@ Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
 [![R-CMD-check](https://github.com/tesselle/tabula/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/tabula/actions)
 [![codecov](https://codecov.io/gh/tesselle/tabula/branch/master/graph/badge.svg)](https://app.codecov.io/gh/tesselle/tabula)
 [![CodeFactor](https://www.codefactor.io/repository/github/tesselle/tabula/badge)](https://www.codefactor.io/repository/github/tesselle/tabula)
-[![Dependencies](https://tinyverse.netlify.com/badge/tabula)](https://cran.r-project.org/package=tabula)
+[![Dependencies](https://tinyverse.netlify.app/badge/tabula)](https://cran.r-project.org/package=tabula)
 
 [![r-universe](https://tesselle.r-universe.dev/badges/tabula)](https://tesselle.r-universe.dev/tabula){.pkgdown-devel}
 [![CRAN Version](http://www.r-pkg.org/badges/version/tabula)](https://cran.r-project.org/package=tabula){.pkgdown-release}
@@ -47,7 +47,9 @@ An easy way to examine archaeological count data. This package provides several
 
 [**kairos**](https://packages.tesselle.org/kairos/) is a companion package to **tabula** that provides functions for chronological modeling and dating of archaeological assemblages from count data.
 
-```{r citation, echo=FALSE, comment=''}
+---
+
+```{r citation, echo=FALSE, comment='', results='asis'}
 cite <- utils::citation("tabula")
 print(cite, bibtex = FALSE)
 ```

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 [![R-CMD-check](https://github.com/tesselle/tabula/workflows/R-CMD-check/badge.svg)](https://github.com/tesselle/tabula/actions)
 [![codecov](https://codecov.io/gh/tesselle/tabula/branch/master/graph/badge.svg)](https://app.codecov.io/gh/tesselle/tabula)
 [![CodeFactor](https://www.codefactor.io/repository/github/tesselle/tabula/badge)](https://www.codefactor.io/repository/github/tesselle/tabula)
-[![Dependencies](https://tinyverse.netlify.com/badge/tabula)](https://cran.r-project.org/package=tabula)
+[![Dependencies](https://tinyverse.netlify.app/badge/tabula)](https://cran.r-project.org/package=tabula)
 
 <a href="https://tesselle.r-universe.dev/tabula"
 class="pkgdown-devel"><img
@@ -62,21 +62,23 @@ thresholds: rank vs. abundance plots, heatmaps, Ford (1962) and Bertin
 package to **tabula** that provides functions for chronological modeling
 and dating of archaeological assemblages from count data.
 
-    To cite tabula in publications use:
+------------------------------------------------------------------------
 
-      Frerebeau N (2019). "tabula: An R Package for Analysis, Seriation,
-      and Visualization of Archaeological Count Data." _Journal of Open
-      Source Software_, *4*(44). doi:10.21105/joss.01821
-      <https://doi.org/10.21105/joss.01821>.
+To cite tabula in publications use:
 
-      Frerebeau N (2023). _tabula: Analysis and Visualization of
-      Archaeological Count Data_. Université Bordeaux Montaigne, Pessac,
-      France. doi:10.5281/zenodo.1489944
-      <https://doi.org/10.5281/zenodo.1489944>, R package version 3.0.1,
-      <https://packages.tesselle.org/tabula/>.
+Frerebeau N (2019). “tabula: An R Package for Analysis, Seriation, and
+Visualization of Archaeological Count Data.” *Journal of Open Source
+Software*, *4*(44). <doi:10.21105/joss.01821>
+<https://doi.org/10.21105/joss.01821>.
 
-    This package is a part of the tesselle project
-    <https://www.tesselle.org>.
+Frerebeau N (2024). *tabula: Analysis and Visualization of
+Archaeological Count Data*. Université Bordeaux Montaigne, Pessac,
+France. <doi:10.5281/zenodo.1489944>
+<https://doi.org/10.5281/zenodo.1489944>, R package version 3.1.0,
+<https://packages.tesselle.org/tabula/>.
+
+This package is a part of the tesselle project
+<https://www.tesselle.org>.
 
 ## Installation
 
@@ -155,7 +157,8 @@ to this project, you agree to abide by its terms.
 
 ## References
 
-<div id="refs" class="references csl-bib-body hanging-indent">
+<div id="refs" class="references csl-bib-body hanging-indent"
+entry-spacing="0">
 
 <div id="ref-bertin1977" class="csl-entry">
 

diff --git a/codemeta.json b/codemeta.json
@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/tesselle/tabula",
   "issueTracker": "https://github.com/tesselle/tabula/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "3.0.1.9000",
+  "version": "3.1.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.3.2 (2023-10-31)",
+  "runtimePlatform": "R version 4.3.3 (2024-02-29)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -91,6 +91,7 @@
       "@type": "SoftwareApplication",
       "identifier": "folio",
       "name": "folio",
+      "version": ">= 1.4.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -103,6 +104,7 @@
       "@type": "SoftwareApplication",
       "identifier": "khroma",
       "name": "khroma",
+      "version": ">= 1.12.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -231,7 +233,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1420.897KB",
+  "fileSize": "1567.107KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -260,7 +262,7 @@
     },
     {
       "@type": "SoftwareSourceCode",
-      "datePublished": "2023",
+      "datePublished": "2024",
       "author": [
         {
           "@type": "Person",
@@ -271,7 +273,7 @@
       "name": "{tabula: Analysis and Visualization of Archaeological Count Data}",
       "identifier": "10.5281/zenodo.1489944",
       "url": "https://packages.tesselle.org/tabula/",
-      "description": "R package version 3.0.1.9000",
+      "description": "R package version 3.1.0",
       "@id": "https://doi.org/10.5281/zenodo.1489944",
       "sameAs": "https://doi.org/10.5281/zenodo.1489944"
     }

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,5 +1,5 @@
 ## Test environments
-* Local R installation: R 4.3.2
+* Local R installation: R 4.3.3
 * 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
@@ -16,7 +16,7 @@ bibentry(
   key          = "R-tabula",
   author       = person("Nicolas", "Frerebeau", role = "aut"),
   title        = "{tabula: Analysis and Visualization of Archaeological Count Data}",
-  year         = "2023",
+  year         = "2024",
   organization = "Université Bordeaux Montaigne",
   address      = "Pessac, France",
   note         = sprintf("R package version %s", meta$Version),

diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/man/tabula-package.Rd b/man/tabula-package.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,25 +1,25 @@
 # Platform
 
-|field    |value                                                                        |
-|:--------|:----------------------------------------------------------------------------|
-|version  |R version 4.3.2 (2023-10-31)                                                 |
-|os       |Ubuntu 22.04.3 LTS                                                           |
-|system   |x86_64, linux-gnu                                                            |
-|ui       |RStudio                                                                      |
-|language |(EN)                                                                         |
-|collate  |fr_FR.UTF-8                                                                  |
-|ctype    |fr_FR.UTF-8                                                                  |
-|tz       |Europe/Paris                                                                 |
-|date     |2023-11-28                                                                   |
-|rstudio  |2023.09.0+463 Desert Sunflower (desktop)                                     |
-|pandoc   |3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) |
+|field    |value                                                                                |
+|:--------|:------------------------------------------------------------------------------------|
+|version  |R version 4.3.3 (2024-02-29)                                                         |
+|os       |Ubuntu 22.04.4 LTS                                                                   |
+|system   |x86_64, linux-gnu                                                                    |
+|ui       |RStudio                                                                              |
+|language |(EN)                                                                                 |
+|collate  |fr_FR.UTF-8                                                                          |
+|ctype    |fr_FR.UTF-8                                                                          |
+|tz       |Europe/Paris                                                                         |
+|date     |2024-05-16                                                                           |
+|rstudio  |2024.04.0+735 Chocolate Cosmos (desktop)                                             |
+|pandoc   |3.1.11 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/x86_64/ (via rmarkdown) |
 
 # Dependencies
 
 |package |old   |new   |Δ  |
 |:-------|:-----|:-----|:--|
-|tabula  |3.0.0 |3.0.1 |*  |
-|arkhe   |1.4.0 |1.4.0 |   |
+|tabula  |3.0.1 |3.1.0 |*  |
+|arkhe   |1.6.0 |1.6.0 |   |
 
 # Revdeps