Description Usage Arguments Details Value Note Author(s) References See Also Examples
Functions vegemite
and tabasco
display compact
community tables. Function vegemite
prints text tables where
species are rows, and each site takes only one column without
spaces. Function tabasco
provides interface for
heatmap
for a colour image
of the
data. The community table can be ordered by explicit indexing, by
environmental variables or results from an ordination or cluster
analysis.
1 2 3 4 5 |
x |
Community data. |
use |
Either a vector, or an object from |
sp.ind, site.ind |
Species and site indices. In |
zero |
Character used for zeros. |
select |
Select a subset of sites. This can be a logical vector
( |
Rowv, Colv |
Re-order dendrograms for the rows (sites) or
columns (species) of |
scale |
Cover scale used (can be abbreviated). |
maxabund |
Maximum abundance used with |
... |
Arguments passed to |
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 +
.
The functions are used mainly to display a table, but they return (invisibly) a list with items:
species |
Ordered species indices |
sites |
Ordered site indices |
These items can be used as arguments sp.ind
and site.ind
to reproduce the table. In addition to the proper table, vegemite
prints the numbers of species and sites and the name of the used cover
scale at the end.
The name vegemite
was chosen because the output is so
compact, and the tabasco
because it is just as compact, but
uses heat colours.
Jari Oksanen
The cover scales are presented in many textbooks of vegetation science; I used:
Shimwell, D.W. (1971) The Description and Classification of Vegetation. Sidgwick & Jackson.
cut
and approx
for making your
own ‘cover scales’ for vegemite
. Function
tabasco
is based on heatmap
which in turn is
based on image
. Both functions order species with
weighted averages using wascores
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | data(varespec)
## Print only more common species
freq <- apply(varespec > 0, 2, sum)
vegemite(varespec, scale="Hult", sp.ind = freq > 10)
## Order by correspondence analysis, use Hill scaling and layout:
dca <- decorana(varespec)
vegemite(varespec, dca, "Hill", zero="-")
## Show one class from cluster analysis, but retain the ordering above
clus <- hclust(vegdist(varespec))
cl <- cutree(clus, 3)
sel <- vegemite(varespec, use=dca, select = cl == 3, scale="Br")
## Re-create previous
vegemite(varespec, sp=sel$sp, site=sel$site, scale="Hult")
## Re-order clusters by ordination
clus <- as.dendrogram(clus)
clus <- reorder(clus, scores(dca, choices=1, display="sites"), agglo.FUN = mean)
vegemite(varespec, clus, scale = "Hult")
## Abundance values have such a wide range that they must be rescaled
## or all abundances will not be shown in tabasco
tabasco(decostand(varespec, "log"), dca)
## Classification trees for species
data(dune, dune.taxon)
taxontree <- hclust(taxa2dist(dune.taxon))
plotree <- hclust(vegdist(dune), "average")
## Automatic reordering of clusters
tabasco(dune, plotree, sp.ind = taxontree)
## No reordering of taxonomy
tabasco(dune, plotree, sp.ind = taxontree, Colv = FALSE)
## Species cluster: most dissimilarity indices do a bad job when
## comparing rare and common species, but Raup-Crick makes sense
sptree <- hclust(vegdist(t(dune), "raup"), "average")
tabasco(dune, plotree, sptree)
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