vegemite {vegan} | R Documentation

## 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` to reorder sites.
`scale` | Cover scale used (can be abbreviated).
`maxabund` | Maximum abundance used with `scale = "log"`. Data maximum in the `select`ed subset will be usd if this is missing.
`...` | Arguments passed to `coverscale` (i.e., `maxabund`).

### 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 `+`.

### 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.

### Note

This function was called `vegetab` in older versions of `vegan`. The new name was chosen because the output is so compact (and to avoid confusion with the `vegtab` function in the labdsv package).

### 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', `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")

[Package vegan version 1.8-6 Index]