Merge branch 'adonis-defunct'

R/adonis-deprecated.R

@@ -5,7 +5,7 @@
              contr.unordered="contr.sum", contr.ordered="contr.poly",
              parallel = getOption("mc.cores"), ...)
 {
-    .Deprecated("adonis2", package="vegan")
+    .Defunct("adonis2", package="vegan")
     EPS <- sqrt(.Machine$double.eps) ## use with >= in permutation P-values
     ## formula is model formula such as Y ~ A + B*C where Y is a data
     ## frame or a matrix, and A, B, and C may be factors or continuous

inst/NEWS.md

@@ -4,6 +4,8 @@
 
 #### DEPRECATED AND DEFUNCT
 
+* `adonis` is defunct: use `adonis2` with improved functionality.
+
 * Disabled use of `summary` to get ordination scores: use `scores`!
   For `summary.cca` see
   [#644](https://github.com/vegandevs/vegan/discussions/644).

man/vegan-defunct.Rd

@@ -21,6 +21,7 @@
 \alias{as.mlm.cca}
 \alias{as.mlm.rda}
 \alias{humpfit}
+\alias{adonis}
 
 %------ NOTE:  ../R/vegan-defunct.R   must be synchronized with this!
 \title{Defunct Functions in Package \pkg{vegan}}
@@ -30,6 +31,11 @@
   \pkg{vegan} as they are no longer needed.
 }
 \usage{
+## defunct in vegan 2.7-0 (development 2.6-7)
+adonis(formula, data, permutations = 999, method = "bray",
+    strata = NULL, contr.unordered = "contr.sum",
+    contr.ordered = "contr.poly", parallel = getOption("mc.cores"), ...)
+
 ## defunct in vegan 2.6-0
 as.mlm(x)
 humpfit(mass, spno, family = poisson, start)
@@ -56,6 +62,12 @@ permuted.index2(n, control = permControl())
 
 \details{
 
+  \code{\link{adonis2}} replaces \code{adonis} with extended
+  functionality and completely new internal design. The shared arguments
+  of \code{adonis} are similar as in \code{\link{adonis2}}, but
+  arguments \code{contr.unordered} and \code{contr.ordered} can set the
+  contrasts within \code{adonis}.
+
   \code{as.mlm} function is replaced with a set functions that can
   find the same statistics directly from the ordination result object:
   see \code{\link{hatvalues.cca}}, \code{\link{rstandard.cca}},

man/vegan-deprecated.Rd

@@ -1,6 +1,5 @@
 \name{vegan-deprecated}
 
-\alias{adonis}
 \alias{orditkplot}
 \alias{plot.orditkplot}
 \alias{scores.orditkplot}
@@ -20,12 +19,7 @@
 }
 
 \usage{
-## use adonis2 instead
-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,  ...)
@@ -41,10 +35,7 @@ as.mcmc.permat(x)
 }
 
 \arguments{
-  \item{formula, data, permutations, method, parallel, \dots}{See
-    \code{\link{adonis2}}.}
-  \item{strata}{groups (strata) within which to constrain permutations.}
-  \item{contr.unordered, contr.ordered}{contrasts used for design matrix.}
+
   \item{x}{ordination result \code{orditkplot} or object to be
      tranformed \code{as.mcmc}.}
   \item{display, choices}{kind of scores and number of axes.}
@@ -54,17 +45,12 @@ as.mcmc.permat(x)
      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}.}
+  \item{\dots}{Other arguments passed to the functions.}
 
 }
 
 \details{
 
-  \code{\link{adonis2}} replaces \code{adonis} with extended
-  functionality and completely new internal design. The shared arguments
-  of \code{adonis} are similar as in \code{\link{adonis2}}, but
-  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.