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.