Prepare for next release

CITATION.cff

@@ -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: 3.0.0
+version: 3.0.1
 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,
@@ -71,7 +71,7 @@ references:
   year: '2023'
   location:
     name: Pessac, France
-  notes: R package version 3.0.0
+  notes: R package version 3.0.0.9000
   url: https://packages.tesselle.org/tabula/
   doi: 10.5281/zenodo.1489944
   institution:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tabula
 Title: Analysis and Visualization of Archaeological Count Data
-Version: 3.0.0.9000
+Version: 3.0.1
 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")),

NEWS.md

@@ -1,4 +1,4 @@
-# tabula 3.0.0.9000
+# tabula 3.0.1
 ## Enhancements
 * Omit axes labels where they would abut or overlap previously drawn labels.
 

R/tabula-package.R

@@ -2,7 +2,7 @@
 #' \tabular{ll}{
 #'  **Package:** \tab tabula \cr
 #'  **Type:** \tab Package \cr
-#'  **Version:** \tab 3.0.0 \cr
+#'  **Version:** \tab 3.0.1 \cr
 #'  **License:** \tab GPL-3 \cr
 #'  **Zenodo:** \tab \doi{10.5281/zenodo.1489944} \cr
 #'  **JOSS:** \tab \doi{10.21105/joss.01821} \cr

README.Rmd

@@ -38,12 +38,12 @@ Sys.setlocale("LC_MESSAGES", 'en_GB.UTF-8') # Force locale
 
 An easy way to examine archaeological count data. This package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson, etc.). It allows to easily visualize count data and statistical thresholds: rank vs. abundance plots, heatmaps, @ford1962 and @bertin1977 diagrams, etc. **tabula** provides methods for:
 
-* Diversity measurement: `heterogeneity()`, `evenness()`, `richness()`, `rarefaction()`, `turnover()`
-* Similarity measurement and co-occurrence: `similarity()`, `occurrence()`
-* Assessing sample size and significance: `bootstrap()`, `jackknife()`, `simulate()`
-* @bertin1977 or @ford1962 (battleship curve) diagrams: `plot_bertin()`, `plot_ford()`
-* Seriograph [@desachy2004]: `seriograph()`
-* Heatmaps: `plot_heatmap()`, `plot_spot()`
+* Diversity measurement: `heterogeneity()`, `evenness()`, `richness()`, `rarefaction()`, `turnover()`.
+* Similarity measurement and co-occurrence: `similarity()`, `occurrence()`.
+* Assessing sample size and significance: `bootstrap()`, `jackknife()`, `simulate()`.
+* @bertin1977 or @ford1962 (battleship curve) diagrams: `plot_bertin()`, `plot_ford()`.
+* Seriograph [@desachy2004]: `seriograph()`, `matrigraph()`.
+* Heatmaps: `plot_heatmap()`, `plot_spot()`.
 
 [**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.
 

README.md

@@ -48,15 +48,15 @@ thresholds: rank vs. abundance plots, heatmaps, Ford (1962) and Bertin
 (1977) diagrams, etc. **tabula** provides methods for:
 
 - Diversity measurement: `heterogeneity()`, `evenness()`, `richness()`,
-  `rarefaction()`, `turnover()`
+  `rarefaction()`, `turnover()`.
 - Similarity measurement and co-occurrence: `similarity()`,
-  `occurrence()`
+  `occurrence()`.
 - Assessing sample size and significance: `bootstrap()`, `jackknife()`,
-  `simulate()`
+  `simulate()`.
 - Bertin (1977) or Ford (1962) (battleship curve) diagrams:
-  `plot_bertin()`, `plot_ford()`
-- Seriograph (Desachy 2004): `seriograph()`
-- Heatmaps: `plot_heatmap()`, `plot_spot()`
+  `plot_bertin()`, `plot_ford()`.
+- Seriograph (Desachy 2004): `seriograph()`, `matrigraph()`.
+- Heatmaps: `plot_heatmap()`, `plot_spot()`.
 
 [**kairos**](https://packages.tesselle.org/kairos/) is a companion
 package to **tabula** that provides functions for chronological modeling
@@ -72,7 +72,7 @@ and dating of archaeological assemblages from count data.
       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 3.0.0,
+      <https://doi.org/10.5281/zenodo.1489944>, R package version 3.0.1,
       <https://packages.tesselle.org/tabula/>.
 
     This package is a part of the tesselle project

codemeta.json

@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/tesselle/tabula",
   "issueTracker": "https://github.com/tesselle/tabula/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "3.0.0.9000",
+  "version": "3.0.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -231,7 +231,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1420.662KB",
+  "fileSize": "1420.85KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -271,7 +271,7 @@
       "name": "{tabula: Analysis and Visualization of Archaeological Count Data}",
       "identifier": "10.5281/zenodo.1489944",
       "url": "https://packages.tesselle.org/tabula/",
-      "description": "R package version 3.0.0.9000",
+      "description": "R package version 3.0.1",
       "@id": "https://doi.org/10.5281/zenodo.1489944",
       "sameAs": "https://doi.org/10.5281/zenodo.1489944"
     }

cran-comments.md

@@ -1,6 +1,6 @@
 ## Test environments
-* Local R installation: R 4.3.1
-* Ubuntu 20.04 (on GitHub Actions): R devel, release, oldrel
+* Local R installation: R 4.3.2
+* 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
 
@@ -14,5 +14,5 @@
 
 We checked 2 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
+ * We saw 0 new problems
+ * We failed to check 0 packages

revdep/README.md

@@ -2,47 +2,24 @@
 
 |field    |value                                                                        |
 |:--------|:----------------------------------------------------------------------------|
-|version  |R version 4.3.1 (2023-06-16)                                                 |
+|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     |2023-08-22                                                                   |
-|rstudio  |2023.06.1+524 Mountain Hydrangea (desktop)                                   |
+|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) |
 
 # Dependencies
 
-|package      |old   |new   |Δ  |
-|:------------|:-----|:-----|:--|
-|tabula       |2.0.0 |3.0.0 |*  |
-|arkhe        |1.2.0 |1.2.0 |   |
-|cli          |3.6.1 |NA    |*  |
-|colorspace   |2.1-0 |NA    |*  |
-|fansi        |1.0.4 |NA    |*  |
-|farver       |2.1.1 |NA    |*  |
-|ggplot2      |3.4.3 |NA    |*  |
-|glue         |1.6.2 |NA    |*  |
-|gtable       |0.3.4 |NA    |*  |
-|isoband      |0.2.7 |NA    |*  |
-|labeling     |0.4.2 |NA    |*  |
-|lifecycle    |1.0.3 |NA    |*  |
-|magrittr     |2.0.3 |NA    |*  |
-|munsell      |0.5.0 |NA    |*  |
-|pillar       |1.9.0 |NA    |*  |
-|pkgconfig    |2.0.3 |NA    |*  |
-|R6           |2.5.1 |NA    |*  |
-|RColorBrewer |1.1-3 |NA    |*  |
-|rlang        |1.1.1 |NA    |*  |
-|scales       |1.2.1 |NA    |*  |
-|tibble       |3.2.1 |NA    |*  |
-|utf8         |1.2.3 |NA    |*  |
-|vctrs        |0.6.3 |NA    |*  |
-|viridisLite  |0.4.2 |NA    |*  |
-|withr        |2.5.0 |NA    |*  |
+|package |old   |new   |Δ  |
+|:-------|:-----|:-----|:--|
+|tabula  |3.0.0 |3.0.1 |*  |
+|arkhe   |1.4.0 |1.4.0 |   |
 
 # Revdeps