Prepare for next release

CITATION.cff

@@ -1,5 +1,5 @@
 # -----------------------------------------------------------
-# CITATION file created with {cffr} R package, v0.2.2
+# CITATION file created with {cffr} R package, v0.2.3
 # 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: 1.7.0.9000
+version: 1.8.0
 abstract: '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.),
@@ -30,7 +30,7 @@ preferred-citation:
     email: nicolas.frerebeau@u-bordeaux-montaigne.fr
     orcid: https://orcid.org/0000-0001-5759-4944
     affiliation: Université Bordeaux Montaigne
-  version: 1.7.0.9000
+  version: 1.8.0
   abstract: '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.),
@@ -50,7 +50,6 @@ preferred-citation:
   - archaeological-science
   - archaeology
   - data-visualization
-  - matrix-seriation
   - r-package
   license: GPL-3.0-or-later
   year: '2022'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tabula
 Title: Analysis and Visualization of Archaeological Count Data
-Version: 1.7.0.9000
+Version: 1.8.0
 Authors@R: 
     c(person(given = "Nicolas",
              family = "Frerebeau",

NEWS.md

@@ -1,4 +1,4 @@
-# tabula 1.7.0.9000
+# tabula 1.8.0
 **Seriation methods are now reexported from kairos and will be removed in a future release.**
 
 ## New classes and methods

R/AllGenerics.R

@@ -288,11 +288,6 @@ setGeneric(
 #' @author N. Frerebeau
 #' @family diversity measures
 #' @docType methods
-#' @name heterogeneity
-#' @rdname heterogeneity
-NULL
-
-#' @rdname heterogeneity
 #' @aliases heterogeneity-method
 setGeneric(
   name = "heterogeneity",
@@ -459,11 +454,6 @@ setGeneric(
 #' @author N. Frerebeau
 #' @family diversity measures
 #' @docType methods
-#' @name richness
-#' @rdname richness
-NULL
-
-#' @rdname richness
 #' @aliases richness-method
 setGeneric(
   name = "richness",
@@ -521,6 +511,7 @@ setGeneric(
   def = function(x, ...) standardGeneric("index_menhinick")
 )
 
+## Rarefaction -----------------------------------------------------------------
 #' Rarefaction
 #'
 #' @param object A \eqn{m \times p}{m x p} `numeric` [`matrix`] or
@@ -556,11 +547,6 @@ setGeneric(
 #' @author N. Frerebeau
 #' @family diversity measures
 #' @docType methods
-#' @name rarefaction
-#' @rdname rarefaction
-NULL
-
-#' @rdname rarefaction
 #' @aliases rarefaction-method
 setGeneric(
   name = "rarefaction",
@@ -639,11 +625,6 @@ setGeneric(
 #' @author N. Frerebeau
 #' @family diversity measures
 #' @docType methods
-#' @name similarity
-#' @rdname similarity
-NULL
-
-#' @rdname similarity
 #' @aliases similarity-method
 setGeneric(
   name = "similarity",
@@ -707,11 +688,6 @@ setGeneric(
 #' @author N. Frerebeau
 #' @family diversity measures
 #' @docType methods
-#' @name occurrence
-#' @rdname occurrence
-NULL
-
-#' @rdname occurrence
 #' @aliases occurrence-method
 setGeneric(
   name = "occurrence",
@@ -766,14 +742,10 @@ setGeneric(
 #' @author N. Frerebeau
 #' @family diversity measures
 #' @docType methods
-#' @name turnover
-#' @rdname turnover
-NULL
-
-#' @rdname turnover
 #' @aliases turnover-method
 setGeneric(
   name = "turnover",
+
   def = function(object, ...) standardGeneric("turnover")
 )
 
@@ -869,6 +841,32 @@ NULL
 #' @rdname plot_diversity
 NULL
 
+## Diversity Test --------------------------------------------------------------
+#' Diversity Test
+#'
+#' Compares Shannon diversity between samples.
+#' @param object A \eqn{m \times p}{m x p} matrix of count data.
+#' @param adjust A [`character`] string specifying the method for
+#'  adjusting \eqn{p} values (see [stats::p.adjust()]).
+#' @param ... Further arguments to be passed to internal methods.
+#' @details
+#'  This test produces two sided pairwise comparisons: it returns a matrix of
+#'  adjusted \eqn{p} values.
+#' @return
+#'  A [`numeric`] [`matrix`].
+#' @example inst/examples/ex-test.R
+#' @author N. Frerebeau
+#' @references
+#'  Magurran, A. E. (1988). *Ecological Diversity and its Measurement*.
+#'  Princeton, NJ: Princeton University Press. \doi{10.1007/978-94-015-7358-0}.
+#' @family statistics
+#' @docType methods
+#' @aliases test_diversity-method
+setGeneric(
+  name = "test_diversity",
+  def = function(object, ...) standardGeneric("test_diversity")
+)
+
 # Plot =========================================================================
 ## Heatmap ---------------------------------------------------------------------
 #' Heatmap
@@ -1056,34 +1054,6 @@ setGeneric(
   def = function(object, ...) standardGeneric("plot_spot")
 )
 
-# Test =========================================================================
-## Diversity Test --------------------------------------------------------------
-#' Diversity Test
-#'
-#' Compares Shannon diversity between samples.
-#' @param object A \eqn{m \times p}{m x p} matrix of count data.
-#' @param adjust A [`character`] string specifying the method for
-#'  adjusting \eqn{p} values (see [stats::p.adjust()]).
-#' @param ... Further arguments to be passed to internal methods.
-#' @details
-#'  This test produces two sided pairwise comparisons: it returns a matrix of
-#'  adjusted \eqn{p} values.
-#' @return
-#'  A [`numeric`] [`matrix`].
-#' @example inst/examples/ex-test.R
-#' @author N. Frerebeau
-#' @references
-#'  Magurran, A. E. (1988). *Ecological Diversity and its Measurement*.
-#'  Princeton, NJ: Princeton University Press. \doi{10.1007/978-94-015-7358-0}.
-#' @family statistics
-#' @docType methods
-#' @rdname test_diversity
-#' @aliases test_diversity-method
-setGeneric(
-  name = "test_diversity",
-  def = function(object, ...) standardGeneric("test_diversity")
-)
-
 # Deprecated ===================================================================
 #' Deprecated Methods
 #'

R/tabula-package.R

@@ -2,7 +2,7 @@
 #' \tabular{ll}{
 #'  **Package:** \tab tabula \cr
 #'  **Type:** \tab Package \cr
-#'  **Version:** \tab 1.7.0 \cr
+#'  **Version:** \tab 1.8.0 \cr
 #'  **License:** \tab GPL-3 \cr
 #'  **Zenodo:** \tab \doi{10.5281/zenodo.1489944} \cr
 #'  **JOSS:** \tab \doi{10.21105/joss.01821} \cr

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": "1.7.0.9000",
+  "version": "1.8.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -250,7 +250,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "1888.796KB",
+  "fileSize": "1888.341KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

cran-comments.md

@@ -1,16 +1,14 @@
 ## Test environments
-* Local R installation: R 4.2.0
+* Local R installation: R 4.2.1
 * Ubuntu 20.04 (on GitHub Actions): R devel, release, oldrel
 * Windows (on GitHub Actions and win-builder): R devel, release, oldrel
 * MacOS (on GitHub Actions): R release
 
 ## R CMD check results
 
-0 errors | 1 warnings | 1 note
+0 errors | 0 warnings | 1 note
 
-* CRAN package check warning ("replacing previous import") has been fixed.
 * Some links in the documentation point to articles behind paywalls that may return a 403 error.
-* This is a resubmission.
 
 ## revdepcheck results