The function vegemite prints a traditional community table.
The display is transposed, so that species are in rows and sites in
columns. The table is printed in compact form: only one character
can be used for abundance, and there are no spaces between
columns. Species with no occurrences are dropped from the table. Function tabasco produces a similar table as vegemite
using heatmap, where abundances are coded by
colours. The function can also display dendrograms for sites
(columns) or species if these are given as an argument (use
for sites, sp.ind for species).
The parameter use will be used to re-order output. The
use can be a vector or an object from hclust or
agnes, a dendrogram or any
ordination result recognized by scores (all ordination
methods in vegan and some of those not in vegan). The
hclust, agnes and
dendrogram must be for sites. The dendrogram is
displayed above the sites in tabasco, but is not shown in
vegemite. No dendrogram for species is displayed, except
when given in sp.ind.
If use is a vector, it is used for ordering sites. If
use is an object from ordination, both sites and species are
arranged by the first axis (provided that results are available both
also for species). When use is an object from
hclust, agnes or a
dendrogram, the sites are ordered similarly as in the
cluster dendrogram. Function tabasco re-orders the
dendrogram if Rowv = TRUE or Rowv is a vector. Such
re-ordering is not available for vegemite, but it can be done
by hand using reorder.dendrogram. In all cases where
species scores are missing, species are ordered by their weighted
averages (wascores) on site order.
Species and sites can be ordered explicitly giving their indices or
names in parameters sp.ind and site.ind. If these are
given, they take precedence over use. A subset of sites can
be displayed using argument select, but this cannot be used
to order sites, but you still must give use or
site.ind. However, tabasco makes two exceptions:
site.ind and select cannot be used when use is
a dendrogram (clustering result). In addition, the sp.ind can
be an hclust tree, agnes
clustering or a dendrogram, and in that case the
dendrogram is plotted on the left side of the
heatmap. Phylogenetic trees cannot be directly used,
as.hclust.phylo (package ape) can transform
these to hclust trees.
If scale is given, vegemite calls
coverscale to transform percent cover
scale or some other scales into traditional class scales used in
vegetation science (coverscale can be called directly, too).
Braun-Blanquet and Domin scales are actually not
strict cover scales, and the limits used for codes r and
+ are arbitrary. Scale Hill may be
inappropriately named, since Mark O. Hill probably never intended this
as a cover scale. However, it is used as default 'cut levels' in his
TWINSPAN, and surprisingly many users stick to this default,
and this is a de facto standard in publications. All
traditional
scales assume that values are cover percentages with maximum 100.
However, non-traditional alternative log can be used with any
scale range. Its class limits are integer powers of 1/2 of the
maximum (argument maxabund), with + used for non-zero entries
less than 1/512 of the maximum (log stands alternatively for
logarithmic or logical). Scale fix is intended for `fixing'
10-point scales: it truncates scale values to integers, and replaces
10 with X and positive values below 1 with +.