seriation: Reorder as to Reflect a Vegetation Table
In vegsoup: Classes and Methods for Phytosociology

Description Usage Arguments Details Value Note Author(s) References See Also Examples

The method rearranges the species matrix according to ordination coordinates, cluster analysis or by species frequencies to achieve a ‘structured’ table following phytosociological principles. A modified object is returned as to reflect the order of plots and species as returned by the selected method.

## S4 method for signature 'Vegsoup'
seriation(obj, method, mode, ...)

## S4 method for signature 'VegsoupPartition'
seriation(obj, method, mode, ...)

`obj`	A `Vegsoup*` object.
`method`	Method applied to obtain new order of data set. If missing defaults to `"dca"`. See ‘Details’.
`mode`	`Q` or `R` mode analysis passed to `as.matrix`.
`...`	Additional arguments passed to `decorana`. See ‘Note’.

For objects of class Vegsoup the default method "dca" uses function decorana in vegan with default settings. Method "hclust" uses hclust with argument method = "ward", "ward" calls agnes with argument method = "ward" and "flexible" invokes agnes with arguments method = "flexible" and par.method = c(0.625, 0.625, 1 - 2 * 0.625, 0). Finally, method "packed" simply performs ordering by row and col sums.

The method defined for class "VegsoupPartition" equals separate calls to subsets defined by partitioning(obj), same as a call to objects of class Vegsoup, followed by final combination of all subsets into a single object. Note that this orders plots within each group based on the defined method, but the order of species is determined by order they appear in single subsets. So the order of species might not be satisfactory.

Ordering by explicit indexing is available by using the method Extract method for Vegsoup* objects.

An object of class depending of the input class.

Currently there are only very limited ways to pass down arguments to functions and. Only presence/absence data is used in. Arguments to method "dca" (decorana, "iweigh", ira, etc. ) can be specified using the "..." argument.

Roland Kaiser

Missing!

vegemite in package vegan for the ancestor of all vegetation table functions, ordcomm for an interactive implementation in package labdsv, and VegsoupPartition for creating a partitions.

require(vegsoup)

data(barmstein)
x <- barmstein

rownames(seriation(x))
rownames(seriation(x, "packed"))

# use default print method of package Matrix
require(Matrix)
# zero are printed as dots and decimals are truncated to 0
t(as(seriation(x, "dca"), "sparseMatrix"))