vegan-deprecated-lattice: Deprecated lattice Functions in vegan

Description

Lattice functions are going to be deprecated and removed from vegan. They are replaced with ggplot2 functions in CRAN package ggvegan.

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, ...)
ordixyplot(x, data = NULL, formula, display = "sites", choices = 1:3,
    panel = "panel.ordi", aspect = "iso", envfit,
    type = c("p", "biplot"), ...)
# S3 method for poolaccum
plot(x, alpha = 0.05, type = c("l","g"), ...)
# S3 method for renyiaccum
plot(x, what = c("Collector", "mean", "Qnt 0.025",
    "Qnt 0.975"),
     type = "l", ...)
permulattice(x, plot = c("densityplot", "qqmath"), observed = TRUE,
    axislab = "Permutations", ...)
# S3 method for permustats
densityplot(x, data, observed = TRUE,
    xlab = "Permutations", ...)
# S3 method for permustats
qqmath(x, data, observed = TRUE, sd.scale = FALSE,
    ylab = "Permutations", ...)

Arguments

x: Input object.
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".
data: Optional data to amend ordination results. The ordination results are found from x, but you may give here data for other variables needed in plots. Typically these are environmental data.
formula: Formula to define the plots. A default formula will be used if this is omitted. The ordination axes must be called by the same names as in the ordination results (and these names vary among methods).
display: The kind of scores: an argument passed to scores.
choices: The axes selected: an argument passed to scores.
panel, prepanel: The name of the panel or prepanel function.
aspect: The aspect of the plot (passed to the lattice function).
envfit: Result of envfit function displayed in ordixyplot. Please note that this needs same choices as ordixyplot.
type: The type of plot. This knows the same alternatives as panel.xyplot. In addition ordixyplot has alternatives "biplot", "arrows" and "polygon". The first displays fitted vectors and factor centroids of envfit, or in constrained ordination, the biplot arrows and factor centroids if envfit is not given. The second (type = "arrows") is a trellis variant of ordiarrows and draws arrows by groups. The line parameters are controlled by trellis.par.set for superpose.line, and the user can set length, angle and ends parameters of panel.arrows. The last one (type = "polygon") draws a polygon enclosing all points in a panel over a polygon enclosing all points in the data. The overall polygon is controlled by Trellis parameters trellis.par.set plot.polygon and superpose.polygon.
what: Items to be plotted.
plot: Use lattice function densityplot or qqmath.
xlab, ylab, axislab: Label for the axis displaying permutation values.
observed: Add observed statistic among permutations.
sd.scale: Scale permutations to unit standard deviation and observed statistic to standardized effect size.
alpha: Level of quantiles shown. This proportion will be left outside symmetric limits.
...: Arguments passed to scores methods or lattice functions.

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. CRAN package ggvegan provides modern alternatives to most lattice functions in vegan. The lattice functions in vegan will be deprecated as soon ggvegan provides a ggplot2 alternative. The deprecated functions will be defunct in the next major release of vegan.

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.
ordixyplot: use autoplot or ordiggplot functions in ggvegan.
plot functions for poolaccum, and renyiaccum: use autoplot or fortify in ggvegan.
permulattice: use autoplot in ggvegan.
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.