Usage
ordihull(ord, groups, display = "sites", draw = c("lines","polygon", "none"), col = NULL, alpha = 127, show.groups, label = FALSE, border = NULL, lty = NULL, lwd = NULL, ...)
ordiellipse(ord, groups, display="sites", kind = c("sd","se", "ehull"), conf, draw = c("lines","polygon", "none"),
w = weights(ord, display), col = NULL, alpha = 127, show.groups,
label = FALSE, border = NULL, lty = NULL, lwd=NULL, ...)
ordibar(ord, groups, display = "sites", kind = c("sd", "se"), conf, w = weights(ord, display), col = 1, show.groups, label = FALSE,
lwd = NULL, length = 0, ...)
ordispider(ord, groups, display="sites", w = weights(ord, display),
spiders = c("centroid", "median"), show.groups, label = FALSE, col = NULL, lty = NULL, lwd = NULL, ...)
ordicluster(ord, cluster, prune = 0, display = "sites", w = weights(ord, display), col = 1, ...)
"summary"(object, ...)
"summary"(object, ...)
ordiareatest(ord, groups, area = c("hull", "ellipse"), kind = "sd", permutations = 999, parallel = getOption("mc.cores"), ...)
Arguments
ord
An ordination object or an ordiplot object. groups
Factor giving the groups for which the graphical item is
drawn.
display
Item to displayed.
draw
Use either lines or polygon
to draw the lines. Graphical parameters are passed to both. The
main difference is that polygons may be filled and
non-transparent. With none nothing is drawn, but the
function returns the invisible plotting data. col
Colour of hull or ellipse lines (if draw = "lines")
or their fills (if draw = "polygon") in ordihull and
ordiellipse. When draw = "polygon", the colour of
bordering lines can be set with argument border of the
polygon function. For other functions the effect
depends on the underlining functions this argument is passed to.
When multiple values of col are specified these are used
for each element of names(table(groups)) (in that order),
shorter vectors are recycled. Function ordicluster has
no groups, and there the argument will be recycled for
points, and the colour of connecting lines is a mixture of point
s in the cluster. alpha
Transparency of the fill colour with draw
= "polygon" in ordihull and ordiellipse. The
argument takes precedence over possible transparency definitions
of the colour. The value must be in range $0...255$, and low
values are more transparent. Transparency is not available in all
graphics devices or file formats.
show.groups
Show only given groups. This can be a vector, or
TRUE if you want to show items for which condition is
TRUE. This argument makes it possible to use different
colours and line types for groups. The default is to show all groups.
label
Label the groups by their names in the centroid
of the object. ordiellipse and ordihull use standard
text, and others use ordilabel. w
Weights used to find the average within group. Weights are
used automatically for cca
and decorana results, unless undone by the
user. w=NULL sets equal weights to all points. kind
Draw standard deviations of points (sd), standard
errors (se) or ellipsoid hulls that enclose all points in
the group (ehull).
conf
Confidence limit for ellipses, e.g. 0.95. If given, the
corresponding sd or se is multiplied with the
corresponding value found from the Chi-squared distribution with
2df.
spiders
Are centres or spider bodies calculated either as
centroids (averages) or spatial medians.
cluster
Result of hierarchic cluster analysis, such as
hclust or agnes. prune
Number of upper level hierarchies removed from the
dendrogram. If prune $>0$, dendrogram will be
disconnected.
object
A result object from ordihull or
ordiellipse. The result is invisible, but it
can be saved, and used for summaries (areas etc. of hulls and
ellipses). area
Evaluate the area of convex hulls of ordihull, or of
ellipses of ordiellipse.
permutations
a list of control values for the permutations
as returned by the function how, or the
number of permutations required, or a permutation matrix where each
row gives the permuted indices. parallel
Number of parallel processes or a predefined socket
cluster. With parallel = 1 uses ordinary, non-parallel
processing. The parallel processing is done with parallel
package.
lty, lwd, border
Vectors of these parameters can be supplied
and will be applied (if appropriate) for each element of
names(table(groups)) (in that order). Shorter vectors will be
recycled.
length
Width (in inches) of the small (“caps”) at the
ends of the bar segment (passed to arrows). ...
Parameters passed to graphical functions or to
scores to select axes and scaling etc.