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.