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
col
our 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 col
ours 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.