version 3.0.1

cran · Nov 29, 2023 · 2cf6f79 · 2cf6f79
1 parent 52210d1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: tabula
 Title: Analysis and Visualization of Archaeological Count Data
-Version: 3.0.0
+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")),
@@ -13,7 +13,9 @@ Authors@R: c(
     person("Anne", "Philippe", , "anne.philippe@univ-nantes.fr", role = "ctb",
            comment = c(ORCID = "0000-0002-5331-5087", affiliation = "Université de Nantes")),
     person("Jean-Baptiste", "Fourvel", , "jean-baptiste.fourvel@univ-amu.fr", role = "ctb",
-           comment = c(ORCID = "0000-0002-1061-4642", affiliation = "CNRS"))
+           comment = c(ORCID = "0000-0002-1061-4642", affiliation = "CNRS")),
+    person("Université Bordeaux Montaigne", role = "fnd"),
+    person("CNRS", role = "fnd")
   )
 Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
 Description: An easy way to examine archaeological count data. This
@@ -28,7 +30,7 @@ URL: https://packages.tesselle.org/tabula/,
         https://github.com/tesselle/tabula
 BugReports: https://github.com/tesselle/tabula/issues
 Depends: R (>= 3.5)
-Imports: arkhe (>= 1.2.0), graphics, grDevices, methods, stats, utils
+Imports: arkhe (>= 1.4.0), graphics, grDevices, methods, stats, utils
 Suggests: folio, khroma, knitr, rmarkdown, rsvg, svglite, tinysnapshot,
         tinytest
 VignetteBuilder: knitr
@@ -45,7 +47,7 @@ Collate: 'AllClasses.R' 'AllGenerics.R' 'coerce.R' 'data.R'
         'show.R' 'statistics.R' 'subset.R' 'tabula-deprecated.R'
         'tabula-internal.R' 'tabula-package.R' 'validate.R' 'zzz.R'
 NeedsCompilation: no
-Packaged: 2023-08-22 13:42:23 UTC; nicolas
+Packaged: 2023-11-28 15:24:55 UTC; nicolas
 Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>,
     Université Bordeaux Montaigne),
   Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>, Université
@@ -57,6 +59,8 @@ Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>,
   Anne Philippe [ctb] (<https://orcid.org/0000-0002-5331-5087>,
     Université de Nantes),
   Jean-Baptiste Fourvel [ctb] (<https://orcid.org/0000-0002-1061-4642>,
-    CNRS)
+    CNRS),
+  Université Bordeaux Montaigne [fnd],
+  CNRS [fnd]
 Repository: CRAN
-Date/Publication: 2023-08-22 15:40:02 UTC
+Date/Publication: 2023-11-28 17:20:02 UTC
diff --git a/MD5 b/MD5
@@ -1,8 +1,8 @@
-2636f1ec1b7ab7bbc893b563d25ee5ce *DESCRIPTION
+d0ca5bb4381c18023efb3c8b81d14a64 *DESCRIPTION
 ac3c6d49d5d63b800b9775134d2621cf *NAMESPACE
-a322c8caf084b350e8fd6355fd20051b *NEWS.md
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 0aab1f5b793b4d3ebadc35df17948b65 *R/AllClasses.R
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@@ -29,24 +29,24 @@ f66be366d8a318633d6f94eb35eb52cf *R/reexport.R
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@@ -125,35 +125,35 @@ a062aa4844028bdf86c16fa7cf35edba *man/RarefactionIndex-class.Rd
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# tabula 3.0.1
+## Enhancements
+* Omit axes labels where they would abut or overlap previously drawn labels.
+
 # tabula 3.0.0
 ## Bugfixes & changes
 * Fix handling of missing values in heterogeneity index (#27).

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -1048,7 +1048,8 @@ setGeneric(
 #'  See `seriograph()`.
 #' @param fill The color for filling the bars.
 #' @param border The color to draw the borders.
-#' @param axes A [`logical`] scalar: should axes be drawn on the plot?
+#' @param axes A [`logical`] scalar: should axes be drawn on the plot? It will
+#'  omit labels where they would abut or overlap previously drawn labels.
 #' @param ... Currently not used.
 #' @return
 #'  `plot_ford()` is called it for its side-effects: it results in a graphic

diff --git a/R/plot_diceleraas.R b/R/plot_diceleraas.R
@@ -45,7 +45,7 @@ setMethod(
 
     ## Save and restore
     mar <- graphics::par("mar")
-    mar[2] <- inch2line(lab, cex = cex.axis) + 0.5
+    mar[2] <- arkhe::inch2line(lab, cex = cex.axis) + 0.5
     old_par <- graphics::par(mar = mar)
     on.exit(graphics::par(old_par))
 

diff --git a/R/plot_ford.R b/R/plot_ford.R
@@ -29,12 +29,12 @@ setMethod(
     font.axis <- graphics::par("font.axis")
 
     ## Save and restore
-    d <- inch2line("M", cex = cex.axis)
+    d <- arkhe::inch2line("M", cex = cex.axis)
     mfrow <- graphics::par("mfrow")
     mar <- graphics::par("mar")
     mar[1] <- 3
-    mar[2] <- inch2line(lab_row, cex = cex.axis)
-    mar[3] <- inch2line(lab_col, cex = cex.axis)
+    mar[2] <- arkhe::inch2line(lab_row, cex = cex.axis)
+    mar[3] <- arkhe::inch2line(lab_col, cex = cex.axis)
     mar[4] <- 0
 
     old_par <- graphics::par(mfrow = mfrow, mar = mar)
@@ -76,14 +76,17 @@ setMethod(
 
     ## Construct axis
     if (axes) {
-      graphics::mtext(lab_row, side = 2, at = seq_row, las = 2, padj = 0.5,
-                      cex = cex.axis, col.axis = col.axis, font = font.axis)
-      graphics::mtext(lab_col, side = 3, at = unique(data$x), las = 2, padj = 0.5,
-                      cex = cex.axis, col.axis = col.axis, font = font.axis)
+      graphics::axis(side = 2, at = seq_row, labels = lab_row, las = 2,
+                     lty = 0, cex.axis = cex.axis, col.axis = col.axis,
+                     font.axis = font.axis)
+      graphics::axis(side = 3, at = unique(data$x), labels = lab_col, las = 2,
+                     lty = 0, cex.axis = cex.axis, col.axis = col.axis,
+                     font.axis = font.axis)
 
       x_axis <- data$x[which.max(data$value)]
       graphics::axis(side = 1, at = c(x_axis - 0.2, x_axis + 0.2), labels = FALSE)
-      graphics::axis(side = 1, at = x_axis, labels = scale_pc(0.2), tick = FALSE)
+      graphics::axis(side = 1, at = x_axis, labels = arkhe::label_percent(0.2),
+                     tick = FALSE)
     }
 
     if (weights) {

diff --git a/R/plot_matrix.R b/R/plot_matrix.R
@@ -25,7 +25,8 @@
 #' @param drop_zero A [`logical`] scalar: should zeros be discarded?
 #' @param col A vector of colors.
 #' @param midpoint A [`numeric`] value specifying the data midpoint.
-#' @param axes A [`logical`] scalar: should axes be drawn on the plot?
+#' @param axes A [`logical`] scalar: should axes be drawn on the plot? It will
+#'  omit labels where they would abut or overlap previously drawn labels.
 #' @param legend A [`logical`] scalar: should a legend be displayed?
 #' @param asp A length-one [`numeric`] vector, giving the aspect ratio
 #'  \eqn{y/x}.
@@ -57,13 +58,13 @@ plot_matrix <- function(object, panel, diag = TRUE, upper = TRUE, lower = TRUE,
   font.axis <- graphics::par("font.axis")
 
   ## Save and restore
-  d <- inch2line("M", cex = cex.axis)
+  d <- arkhe::inch2line("M", cex = cex.axis)
   old_par <- graphics::par("mar", "plt")
   on.exit(graphics::par(old_par))
 
-  mar_left <- inch2line(lab_row, cex = cex.axis)
-  mar_top <- inch2line(lab_col, cex = cex.axis)
-  mar_right <- if (legend) inch2line("999%", cex = cex.axis) else d
+  mar_left <- arkhe::inch2line(lab_row, cex = cex.axis)
+  mar_top <- arkhe::inch2line(lab_col, cex = cex.axis)
+  mar_right <- if (legend) arkhe::inch2line("999%", cex = cex.axis) else d
   graphics::par(mar = c(d, mar_left, mar_top, mar_right))
 
   ## Open new window
@@ -101,17 +102,19 @@ plot_matrix <- function(object, panel, diag = TRUE, upper = TRUE, lower = TRUE,
 
   ## Construct axis
   if (axes) {
-    graphics::mtext(lab_row, side = 2, at = seq_row, las = 2, padj = 0.5,
-                    cex = cex.axis, col.axis = col.axis, font = font.axis)
-    graphics::mtext(lab_col, side = 3, at = seq_col, las = 2, padj = 0.5,
-                    cex = cex.axis, col.axis = col.axis, font = font.axis)
+    graphics::axis(side = 2, at = seq_row, labels = lab_row, las = 2,
+                   lty = 0, cex.axis = cex.axis, col.axis = col.axis,
+                   font.axis = font.axis)
+    graphics::axis(side = 3, at = seq_col, labels = lab_col, las = 2,
+                   lty = 0, cex.axis = cex.axis, col.axis = col.axis,
+                   font.axis = font.axis)
   }
 
   ## Legend
   if (legend) {
     legend <- attr(data, "legend")
     legend_image <- grDevices::as.raster(legend$colors)
-    legend_y <- scale_range(legend$at) * n + 0.5
+    legend_y <- arkhe::scale_range(legend$at) * n + 0.5
 
     graphics::rasterImage(legend_image, xleft = m + 1, ybottom = max(legend_y),
                           xright = m + 1.5, ytop = min(legend_y))
@@ -187,10 +190,11 @@ panel_tiles <- function(x, y, color, ...) {
 panel_spot <- function(x, y, z, color, type, ...) {
   radius <- abs(z * 0.45)
   for (i in seq_along(x)) {
-    plot_circle(x = x[i], y = y[i], radius = radius[i], col = color[i],
-                border = color[i])
+    arkhe::circle(x = x[i], y = y[i], radius = radius[i],
+                  col = color[i], border = color[i])
     if (type == "ring") {
-      plot_circle(x = x[i], y = y[i], radius = 0.45, col = NA, border = "black")
+      arkhe::circle(x = x[i], y = y[i], radius = 0.45,
+                    col = NA, border = "black")
     }
   }
 }
@@ -303,7 +307,7 @@ prepare <- function(object, diag = TRUE, upper = TRUE, lower = TRUE,
 
   legend_lab[!is.element(legend_lab, legend_brk)] <- NA
   attr(data, "legend") <- list(
-    labels = if (freq) scale_pc(legend_lab) else legend_lab,
+    labels = if (freq) arkhe::label_percent(legend_lab) else legend_lab,
     at = legend_pos,
     colors = legend_col
   )