coldiss: Plots of the Dissimilarity Matrix of an Object of class...

In vegsoup: Classes and Methods for Phytosociology

Description

The method returns two plots corresponding to an unordered and an ordered colored matrix of dissimilarities.

Usage

## S4 method for signature 'Vegsoup'
coldiss(obj, colors, byrank = TRUE, diag = FALSE, method = "dca",
		ordered.only = FALSE, translate = FALSE, ...)

Arguments

obj	An object of class Vegsoup*.
colors	The number of colors, or a vector of colors. See ‘Details’.
byrank	Boolean, if TRUE create equal-sized categories, if FALSE find equal-length intervals.
diag	Boolean, if TRUE annotae the diagonal of the colored matrix.
method	Method argument passed to seriation.
ordered.only	Only display the ordered dissimilarity matrix. Defaults to FALSE.
translate	Display scientific taxon names as defined in taxonomy(obj). Defaults to FALSE and only applies if additional argument mode is supplied and it's value is "R", setting up a R mode analysis. See ‘Examples’.
...	Arguments passed to as.dist. See ‘Examples’.

Details

If colors is a single integer, the argument determines the number of colors to be used with cm.colors. If colors is vector of colors longer than 1 those colors will be used. The function uses dmat.color and order.single in package gclus.

Author(s)

Roland Kaiser, implemented for vegsoup inspired by code in colldiss.R by Francois Gillet supplied with the Book Numerical Ecology with R (Borcard et al. 2011)

References

Borcard, D., Gillet, F., and Legendre, P. (2011). Numerical Ecology with R. Springer.

See Also

dmat.color in package gclus

Examples

require(vegsoup)

data(barmstein)
x <- barmstein

coldiss(x) # default

# other dissimilarity
vegdist(x) <- "bray"
coldiss(x, 4)

# more colors
require(RColorBrewer)

cols <- colorRampPalette(RColorBrewer::brewer.pal(11, "Spectral"))

coldiss(x, cols(4), byrank = FALSE, diag = TRUE)

# R-mode analysis, see ?as.dist
# first collapse layers
x.0l <- layers(x, aggregate = "layer",
				 collapse = "0l", verbose = TRUE)
decostand(x.0l) <- "chi.square"
vegdist(x.0l) 

## Not run: 
# annotate scientific species names
# label only the diagonal to avoid cluttered display
# mode = "R" defunct due to generic dispatch of as.dist(x)
coldiss(dta.0l, rev(cols(20)), mode = "R",
	ordered.only = TRUE, translate = TRUE, diag = TRUE)

## End(Not run)

vegsoup documentation built on Feb. 24, 2021, 3 a.m.