Deprecated lattice Functions in vegan — vegan-deprecated-lattice • vegan

Lattice functions are going to be deprecated and removed from vegan as soon as viable alternatives are available (or if they are unsatisfactory originally).

Usage

ordicloud(x, data = NULL, formula, display = "sites", choices = 1:3,
    panel = "panel.ordi3d", prepanel = "prepanel.ordi3d", ...)
  ordisplom(x, data = NULL, formula = NULL, display = "sites", choices = 1:3, 
    panel = "panel.ordi", type = "p", ...)
  ordiresids(x, kind = c("residuals", "scale", "qqmath"),
    residuals = "working", type = c("p", "smooth", "g"),
    formula, ...)

Arguments

x, data, formula, display, choices, panel, prepanel, type, ...: Similar parameters as in ordixyplot.
kind: The type of plot: residuals or absolute values of residuals against fitted values, or quantile plot of residuals with qqmath.
residuals: The type of residuals with choices "working", "response", "standardized" and "studentized".

Details

Trellis (or lattice) functions were added to vegan mostly in 2008 to 2009. In that time they were the only alternative of the kind, but now there are better, more versatile and more user-friendly alternatives, mainly in ggplot2. The lattice functions will be removed from vegan as soon as we can propose better modern alternatives.

The following functions are currently deprecated:

ordicloud was transferred to vegan3d as ordilattice3d.
ordisplom design is bad and deficient. If you want to have something similar, write your own code.
ordiresids is not very useful, but you can directly access ordination results with fitted.cca, residuals.cca, rstandard.cca, rstudent.cca and other functions that were not available in ordiresids.