vegan-deprecated {vegan}

Deprecated Functions in vegan package

Description

These functions are provided for compatibility with older versions of vegan only, and may be defunct as soon as the next release.

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,  ...)
## S3 method for class 'orditkplot'
plot(x, ...)
## S3 method for class 'orditkplot'
points(x, pch = x$args$pch, cex = x$args$pcex,
       col = x$args$pcol, bg = x$args$pbg, ...)
## S3 method for class 'orditkplot'
text(x, cex = x$args$tcex, col = x$args$tcol,
     font = attr(x$labels, "font"), ...)
## S3 method for class 'orditkplot'
scores(x, display, ...)
## use toCoda instead
as.mcmc.oecosimu(x)
as.mcmc.permat(x)

Arguments

formula, data, permutations, method, parallel, ...

See adonis2.

strata

groups (strata) within which to constrain permutations.

contr.unordered, contr.ordered

contrasts used for design matrix.

x

ordination result orditkplot or object to be tranformed as.mcmc.

display, choices

kind of scores and number of axes.

width

size of Tcl/Tk window in inches.

xlim, ylim, tcex, tcol, pch, pcol, pbg, pcex, labels, cex, col, bg, font

graphical parameters similar to standard plot functions; those applied only to points preceded with p, and those to text with t.

Details

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.

See Also

Deprecated