vegemite: Display Compact Ordered Community Tables

In vegan: Community Ecology Package

Display Compact Ordered Community Tables

Description

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.

Usage

vegemite(x, use, scale, sp.ind, site.ind, zero=".", select ,...)
tabasco(x, use, sp.ind = NULL, site.ind = NULL, select,
    Rowv = TRUE, Colv = TRUE, labRow = NULL, labCol = NULL,
    scale, col = heat.colors(12), ...)
coverscale(x, scale=c("Braun.Blanquet", "Domin", "Hult", "Hill", "fix","log"),
           maxabund, character = TRUE)

Arguments

x	Community data.
use	Either a vector, or an object from cca, decorana etc. or hclust or a dendrogram for ordering sites and species.
sp.ind, site.ind	Species and site indices. In tabasco, these can also be hclust tree, agnes clusterings or dendrograms.
zero	Character used for zeros.
select	Select a subset of sites. This can be a logical vector (TRUE for selected sites), or a vector of indices of selected sites. The order of indices does not influence results, but you must specify use or site.ind to reorder sites.
Rowv, Colv	Re-order dendrograms for the rows (sites) or columns (species) of x. If the Rowv = TRUE, row dendrograms are ordered by the first axis of correspondence analysis, and when Colv = TRUE column dendrograms by the weighted average (wascores) of the row order. Alternatively, the arguments can be vectors that are used to reorder the dendrogram.
labRow, labCol	character vectors with row and column labels used in the heatmap instead of the default. NB., the input matrix is transposed so that row labels will be used for data columns.
scale	In vegemite and coverscale: cover scale used (can be abbreviated). In tabasco: scaling of colours in heatmap. The alternatives of coverscale can be used in tabasco, and in addition "column" or "row" scale columns or rows to equal maxima (NB., these refer to the transposed data of the heatmap), while "none" uses original values.
col	A vector of colours used for above-zero abundance values.
maxabund	Maximum abundance used with scale = "log". Data maximum in the selected subset will be used if this is missing.
character	Return character codes suitable for vegemite. If FALSE, returns corresponding integers.
...	Arguments passed to coverscale (i.e., maxabund) in vegemite and to heatmap in tabasco.

Details

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 scales the abundances to equal intervals for colour palette, but either rows or columns can be scaled to equal maxima, or the coverscale class systems can be used. 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 or reorder.hclust. Please note that dendrogram and hclust reordering can differ: unweighted means of merged branches are used in dendrogram, but weighted means (= means of leaves of the cluster) are used in reorder.hclust. 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, but package ape has tools to 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). Function tabasco can also use these traditional class scales, but it treats the transformed values as corresponding integers. 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 +.

Value

The functions are used mainly to display a table, but they return (invisibly) a list with items species for ordered species index, sites for ordered site index, and table for the final ordered community table.

These items can be used as arguments sp.ind and site.ind to reproduce the table, or the table can be further edited. In addition to the table, vegemite prints the numbers of species and sites and the name of the used cover scale.

Note

The name vegemite was chosen because the output is so compact, and the tabasco because it is just as compact, but uses heat colours.

Author(s)

Jari Oksanen

References

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.

See Also

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.

Examples

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
tabasco(varespec, dca, scale="Braun")

## 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)

vegan documentation built on Sept. 11, 2024, 7:57 p.m.