splitAbbr: Deparse Species Layer Replication of 'Vegsoup*' Objects

In vegsoup: Classes and Methods for Phytosociology

Description

Deparse the layer replications (pseudo-species) used as colnames in the species matrix of Vegsoup* objects into it's components.

Usage

## S4 method for signature 'Vegsoup'
splitAbbr(obj)

decode(x, obj)

Arguments

obj	Vegsoup* object.
x	data.frame, matrix, list, or vector with dimnames.

Details

The splitAbbr method decomposes the colnames of the species matrix into three components. The first giving the taxon abbreviation only (abbr), the second the layer code (layer) and the last component corresponds to the full taxon name (taxon) as queried from taxonomy(obj).

The compound taxon key (abbr.layer) can be accessed from the rownames of the resulting object. This is advantageous as it provides an easy means of subsetting with colnames(obj).

decode is equivalent to the above method, but works for base classes (see ‘Examples’). However, an appropriate Vegsoup or Taxonomy object has to be supplied to query scientific taxon names.

Vegsoup and Species construct these compound taxon abbreviations by pasting make.names(x) and layer seperated with "@". To deparse the abbreviation and layer string splitAbbr should be used.

Value

A "data.frame" with as many rows and in the same order as there are columns in the species matrix. Note, the method uses invisible when returning it's results.

Author(s)

Roland Kaiser

See Also

Vegsoup Taxonomy taxalist taxon

Examples

require(vegsoup)

data(barmstein)
x <- barmstein

# deparse compund taxon and layer replicates
a <- splitAbbr(x)
head(a)

all.equal(rownames(a), colnames(x))

# get scientific taxa names for the columns of the species matrix
# as.matrix returns a species matrix from an 'Vegsoup' object
# we use mode = "R" for instantaneous matrix transposition 
m <- as.matrix(x, typeof = "character", mode = "R")
head(a[rownames(m), ])

# for a unique list of taxa
taxon(x)

# similar result but a matrix
head(taxalist(x, layered = TRUE))

# species matrix including taxon names and layers
m <- cbind(a[rownames(m), ], m)

# and this can be converted bach to class 'Species'
( stackSpecies(m) )

# indexing of 'Vegsoup' object by suppling indices of the the species matrix
# elements according to 'as.matrix' method
x[, rownames(a)[sample(1:ncol(x), 10)]]

# decode rownames of matrix ...
class(xx <- constancy(x))
decode(xx, x)
rownames(xx) <- apply(sapply(decode(xx, x)[c("taxon", "layer")], paste), 1, paste, collapse = "@")
head(xx)

# ... data.frame and Taxonomy object
class(xx <- splitAbbr(x))
decode(xx, taxonomy(x))

# character vector without layer encoded with '@'
decode(taxalist(x)$abbr, x)

# a named list
decode(spread(VegsoupPartition(x, k = 2)), x)

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