vegan (version 2.0-4)

vegemite: Prints a Compact, Ordered Vegetation Table

Description

The function prints a compact vegetation table, where species are rows, and each site takes only one column without spaces. The vegetation 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 ,...)
coverscale(x, scale=c("Braun.Blanquet", "Domin", "Hult", "Hill", "fix","log"),
           maxabund)

Arguments

x

Vegetation data.

use

Either a vector, or an object from cca, decorana etc. or hclust or a dendrogram for ordering sites and species.

sp.ind

Species indices.

site.ind

Site indices.

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

scale

Cover scale used (can be abbreviated).

maxabund

Maximum abundance used with scale = "log". Data maximum in the selected subset will be used if this is missing.

...

Arguments passed to coverscale (i.e., maxabund).

Value

• The function is used mainly to print a table, but it returns (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, the function prints the numbers of species and sites and the name of the used cover scale at the end.

Details

The function prints a traditional vegetation table. Unlike in ordinary data matrices, species are used as rows and sites as 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.

The parameter use can be a vector or an object from hclust, a dendrogram or any ordination result recognized by scores (all ordination methods in vegan and some of those not in vegan). 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. When use is an object from hclust or a dendrogram, the sites are ordered similarly as in the cluster dendrogram. If ordination methods provide species scores, these are used for ordering species. In all cases where species scores are missing, species are ordered by their weighted averages (wascores) on site scores. There is no natural, unique ordering in hierarchic clustering, but in some cases species are still nicely ordered (please note that you can reorder.dendrogram to have such a natural order). Alternatively, 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.

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 +.

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', wascores for weighted averages.

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")