These functions are provided for compatibility with older versions of vegan only, and may be defunct as soon as the next release.
## 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, ...)
# S3 method for orditkplot
plot(x, ...)
# S3 method for orditkplot
points(x, pch = x$args$pch, cex = x$args$pcex,
col = x$args$pcol, bg = x$args$pbg, ...)
# S3 method for orditkplot
text(x, cex = x$args$tcex, col = x$args$tcol,
font = attr(x$labels, "font"), ...)
# S3 method for orditkplot
scores(x, display, ...)
## use toCoda instead
as.mcmc.oecosimu(x)
as.mcmc.permat(x)
See
adonis2.
groups (strata) within which to constrain permutations.
contrasts used for design matrix.
ordination result orditkplot or object to be
tranformed as.mcmc.
kind of scores and number of axes.
size of Tcl/Tk window in inches.
graphical parameters similar to standard
plot functions; those applied only to points preceded with
p, and those to text with t.
adonis2 replaces adonis with extended
functionality and completely new internal design. The shared arguments
of adonis are similar as in adonis2, but
arguments contr.unordered and contr.ordered can set the
contrasts within adonis.
orditkplot was moved to vegan3d (version
1.3-0). Install that package from CRAN and use in the old way.