diff --git a/R/adonis-deprecated.R b/R/adonis-deprecated.R index bf02efbb2..ef06c0d38 100644 --- a/R/adonis-deprecated.R +++ b/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 diff --git a/inst/NEWS.md b/inst/NEWS.md index a6338d22c..b8dbad50d 100644 --- a/inst/NEWS.md +++ b/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). diff --git a/man/vegan-defunct.Rd b/man/vegan-defunct.Rd index bb5d03058..be900146c 100644 --- a/man/vegan-defunct.Rd +++ b/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}}, diff --git a/man/vegan-deprecated.Rd b/man/vegan-deprecated.Rd index d851f732c..353b80e11 100644 --- a/man/vegan-deprecated.Rd +++ b/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.