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=".")
coverscale(x, scale=c("Braun.Blanquet", "Domin", "Hult", "Hill", "fix", "log"))

Arguments

Vegetation data.

use

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

sp.ind

Species indices.

site.ind

Site indices.

zero

Character used for zeros.

scale

Cover scale used (can be abbreviated).

Value

The function is used mainly to print a table, but it returns (invisibly) a list with items:
specOrdered species indices.
sitesOrdered site indices.

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.

The parameter use can be a vector or an object from hclust or any ordination result recognized by scores. 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, 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. 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.

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 so 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 observed maximum in the data, with + used for non-zero entries less than 1/512 of data 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.

Examples

Run this code

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="-")

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