Merge branch 'vegan3d-updates'

DESCRIPTION

@@ -36,7 +36,7 @@ Authors@R: c(person("Jari", "Oksanen", role=c("aut","cre"),
 	   person("Adrian", "Stier", role="aut"),
 	   person("Cajo J.F.", "Ter Braak", role="aut"),
 	   person("James", "Weedon", role="aut"))
-Depends: permute (>= 0.9-0), lattice, R (>= 3.6.0)
+Depends: permute (>= 0.9-0), lattice, R (>= 4.1.0)
 Suggests: parallel, tcltk, knitr, markdown
 Imports: MASS, cluster, mgcv
 VignetteBuilder: utils, knitr

R/orditkplot.R

@@ -10,6 +10,14 @@
         stop("your R has no capability for Tcl/Tk")
     requireNamespace("tcltk") || stop("requires package tcltk")
 
+### orditkplot was moved to vegan3d and is in CRAN since vegan3d_1.3-0
+### (2024-03-19)
+
+    tcltk::tkmessageBox(message = "orditkplot is deprecated",
+                 detail = "function was moved to CRAN package vegan3d",
+                 icon = "warning",
+                 type = "ok")
+
 ############################
 ### Check and sanitize input
 ###########################

R/plot.orditkplot.R

@@ -1,6 +1,7 @@
 `plot.orditkplot` <-
     function(x, ...)
 {
+    .Deprecated(msg = "function was moved to CRAN package vegan3d")
     op <- par(x$par)
     on.exit(par(op))
     plot(x$points, pch = x$args$pch, cex = x$args$pcex, col = x$args$pcol,

R/points.orditkplot.R

@@ -1,5 +1,7 @@
 `points.orditkplot` <- function(x, pch = x$args$pch, cex = x$args$pcex,
-                                col = x$args$pcol, bg = x$args$pbg, ...) {
+                                col = x$args$pcol, bg = x$args$pbg, ...)
+{
+    .Deprecated(msg = "function was moved to CRAN package vegan3d")
     points(x$points, pch = pch, cex = cex, col = col, bg = bg, ...)
 }
 

R/scores.orditkplot.R

@@ -1,6 +1,7 @@
 `scores.orditkplot` <-
     function(x, display, ...)
 {
+    .Deprecated(msg = "function was moved to CRAN package vegan3d")
     if (!missing(display) && !is.na(pmatch(display, "labels")))
         x$labels
     else

R/text.orditkplot.R

@@ -1,5 +1,7 @@
 `text.orditkplot` <- function(x, cex = x$args$tcex, col = x$args$tcol,
-                              font = attr(x$labels, "font"), ...) {
+                              font = attr(x$labels, "font"), ...)
+{
+    .Deprecated(msg = "function was moved to CRAN package vegan3d")
     if (is.null(font)) {
         font <- par("font")
     }

man/ordiplot.Rd

@@ -124,8 +124,7 @@ pl <- ordiplot(dune.mds, type = "none")
 points(pl, "sites", pch=21, col="red", bg="yellow")
 text(pl, "species", col="blue", cex=0.9)
 \dontrun{
-## same plot using pipes (pipes |> are available from R version 4.1.0)
-if (getRversion() >= "4.1") {
+## same plot using pipes (|>)
 ordiplot(dune.mds, type="n") |>
   points("sites", pch=21, col="red", bg="yellow") |>
   text("species", col="blue", cex=0.9)
@@ -137,7 +136,6 @@ plot(mod, type="n") |>
   points("sites", pch=16, col="red") |>
   text("species", arrows = TRUE, length=0.05, col="blue")
 }
-}
 ## Default plot of the previous using identify to label selected points
 \dontrun{
 pl <- ordiplot(dune.mds)

man/vegan-deprecated.Rd

@@ -1,6 +1,11 @@
 \name{vegan-deprecated}
 
 \alias{adonis}
+\alias{orditkplot}
+\alias{plot.orditkplot}
+\alias{scores.orditkplot}
+\alias{points.orditkplot}
+\alias{text.orditkplot}
 \alias{as.mcmc.oecosimu}
 \alias{as.mcmc.permat}
 \alias{vegan-deprecated}
@@ -19,6 +24,17 @@
 adonis(formula, data, permutations = 999, method = "bray",
     strata = NULL, contr.unordered = "contr.sum",
     contr.ordered = "contr.poly", parallel = getOption("mc.cores"), ...)
+    orditkplot(x, display = "species", choices = 1:2, width, xlim, ylim, 
+   tcex = 0.8, tcol, pch = 1,  pcol, pbg, pcex = 0.7, labels,  ...)
+## moved to vegan3d package: install from CRAN
+orditkplot(x, display = "species", choices = 1:2, width, xlim, ylim, 
+   tcex = 0.8, tcol, pch = 1,  pcol, pbg, pcex = 0.7, labels,  ...)
+\method{plot}{orditkplot}(x, ...)
+\method{points}{orditkplot}(x, pch = x$args$pch, cex = x$args$pcex,
+       col = x$args$pcol, bg = x$args$pbg, ...)
+\method{text}{orditkplot}(x, cex = x$args$tcex, col = x$args$tcol,
+     font = attr(x$labels, "font"), ...)
+\method{scores}{orditkplot}(x, display, ...)
 ## use toCoda instead
 as.mcmc.oecosimu(x)
 as.mcmc.permat(x)
@@ -29,7 +45,16 @@ as.mcmc.permat(x)
     \code{\link{adonis2}}.}
   \item{strata}{groups (strata) within which to constrain permutations.}
   \item{contr.unordered, contr.ordered}{contrasts used for design matrix.}
-  \item{x}{object to be tranformed.}
+  \item{x}{ordination result \code{orditkplot} or object to be
+     tranformed \code{as.mcmc}.}
+  \item{display, choices}{kind of scores and number of axes.}
+  \item{width}{size of Tcl/Tk window in inches.}
+
+  \item{xlim, ylim, tcex, tcol, pch, pcol, pbg, pcex, labels, cex,
+     col, bg, font}{graphical parameters similar to standard
+     \code{plot} functions; those applied only to points preceded with
+     \code{p}, and those to text with \code{t}.}
+
 }
 
 \details{
@@ -40,6 +65,9 @@ as.mcmc.permat(x)
   arguments \code{contr.unordered} and \code{contr.ordered} can set the
   contrasts within \code{adonis}.
 
+  \code{orditkplot} was moved to \CRANpkg{vegan3d} (version
+  1.3-0). Install that package from CRAN and use in the old way.
+
 }
 
 \seealso{