orditkplot: R 4.4.0 deprecated XFig device, and it
was defunct and removed in R 4.5.0.
ordilattice3d failed with vegan
2.8-0 or later.
New function ordilattice3d for 3D ordination
graphics using lattice package. The function is
rudimentary and cannot display biplot arrows or centroids. The only
advantage over ordiplot3d is that the output can be
“faceted” or split into panels by external variables.
The function was transferred from vegan where it has been since 2008 (CRAN release 1.11-0).
The function adds a new dependency on lattice package.
ordiplot3d defaults to order axes as horizontal,
vertical and “depth” so that the front panel is similar as in
conventional 2D plots.
ordirgl failed with argument envfit.
Bug report #11.
Fixes minor CRAN issues on cross-references to other packages in manual pages.
New function orditkplot with its support functions
for interactive ordination plots. The function will open a new Tcl/Tk
window where points are fixed at their ordination scores, but their
labels can be moved to better position with mouse or edited. The plot
can be exported in various graphics formats or saved in the
R session for further manipulation or re-created with
R commands.
The function was transferred from vegan where it has been since 2008 (CRAN release 1.11-0).
The function adds a conditional dependency on tcltk package.
ordiplot3d failed if input was a scores matrix
instead of being a list-style object.
rgl.isomap could fail mysteriously with some extra
arguments (e.g. with type = "p").
ordiplot3d can now set the exact aspect ratio in
ordination plots. Earlier we had a kluge that gave approximately correct
ratio. The package now depends on scatterplot3d version
0.3-40.ordirgl failed when cex was a variable
instead of a number.
orglcluster did not obey display
argument but always showed "sites".
orglellipse gained a new option
kind = "ehull" to draw ellipsoid hulls or minimum volume
ellipsoids that enclose all points of a group. The option
is based on ellipsoidhull() function
(cluster package).
ordirgl allows suppressing display of environmental
variables in constrained ordination with
envfit = NA.
orglspider was not exported.orditree3d (based on scatterplot3d)
and ordirgltree (based on rgl) draw a
cluster dendrogram over a 2D ordination or any other plane, for instance
a map.
orglcluster is similar to vegan
ordicluster and adds a cluster dendrogam to an
ordirgl plot.
orglellipse is similar to vegan
ordiellipse and adds standard deviation, standard error or
confidence ellipsoids to an ordirgl plot.
orglspantree is similar to vegan
lines.spantree and adds a minimum spanning tree to an
ordirgl plot.
Users have improved control of colours of plotted items. The
colour can be a vector for points or text items plotted, or
for groups of items drawn in the graph
(orglellipse, orglsegments,
orglspider). If the functions draws lines connecting
points, the line colour is a mixture of colours of
connected points (orditree3d, ordirgltree,
orglcluster, orglspantree,
rgl.isomap).
ordirgl uses now small spheres instead of points
with better visual impact.
ordiplot3d gained a scores function
making easier to add 2D items with vegan
ordiellipse, ordihull,
ordispider, ordisegments etc.
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