Vegsoup-class: Class Vegsoup
In vegsoup: Classes and Methods for Phytosociology

Description Objects from the Class Slots Methods Note Author(s) See Also Examples

This is the foundation class of all Vegsoup* objects.

Objects can be created by calls of the form new("Vegsoup", ...). The user is encouraged to use the creator function Vegsoup.

species:: Object of class Species, the species data in long format.
sites:: Object of class data.frame, the sites data in wide format, developed from class Sites in long format.
taxonomy:: Object of class Taxonomy, the taxonomic reference list.
coverscale:: Object of class Coverscale, the description of the cover scale. See Coverscale for details.
decostand:: character, the method for decostand in vegan. Takes effect if as.matrix or as.dist is called. The slot 'decostand' is in fact of class decostand, this class is not exposed to the user and hence not documented.
dist:: character, giving a method for vegdist. Takes effect in calls or dispatch of as.dist.
layers:: character, containing the (vegetation) layers the object is structured by. Order matters.
group:: integer, a vector of a-priori group assignments.
sp.points:: Object of class SpatialPointsDataFrame defined in package sp. See also SpatialPoints
sp.polygons:: Object of class SpatialPolygonsDataFrame. See also SpatialPolygons.

Classes VegsoupOptimstride, VegsoupPartition and "VegsoupPartitionFidelity" all contain and directly extend class Vegsoup. The methods presented in the following sections apply to all these classes.

1) Dimensions of the object (species matrix).

dim: signature(x = "Vegsoup"): returns matrix dimensions (see above) giving the number of plots and (pseudo-)species.
ncol: signature(x = "Vegsoup"): the number of (pseudo-)species.
nrow: signature(x = "Vegsoup"): the number of plots.
ncell: signature(x = "Vegsoup"): the number of cells in the species matrix.
MatrixFill: signature(obj = "Vegsoup"): the percentage of presences in the species matrix.

2) Layer structure.

layer: signature(obj = "Vegsoup"): returns the layer for each species observation.
layers: signature(obj = "Vegsoup"): modifies an object's layer structure by suppling a layer combination rule as a "character" vector 'collapse'.
layers<-: signature(obj = "Vegsoup"): modifies the order of layers. This has effects on as.matrix and similar.

3) Cover scale.

coverscale: signature(obj = "Vegsoup"): returns the cover scale.
coverscale<-: signature(obj = "Vegsoup", value = "character"): sets the coverscale by suppling a name as recognized by the class creator function Coverscale. signature(obj = "Vegsoup", value = "Coverscale"): sets the coverscale by suppling a "Coverscale" object.
BraunBlanquetReduce: signature(obj = "Vegsoup"): reduce 9 point Braun-Blanquet scale to 7 point.

4) Standardization methods.

decostand: signature(obj = "Vegsoup"): returns the standardization method active for an object.
decostand<-: signature(obj = "Vegsoup", value = "character"): sets the standardization method active for an object. Note, values of slot 'decostand' have effect in as.matrix and similar matrix methods. signature(obj = "Vegsoup", value = "NULL"): reset/remove the standardization for an object by setting the value to NULL.

5) Dissimilarity/distance index.

vegdist: signature(x = "Vegsoup"): returns the dissimilarity/distance index set for an object.
vegdist<-: signature(x = "Vegsoup", value = "character"): set a distance measure for an object.
distconnected: signature(x = "Vegsoup"): connectedness of Dissimilarities.

6) Retrieve indices to species matrix.

indices: signature(x = "Vegsoup"): returns the locations (row and column pointers) and values of all nonzero entries in a species matrix (see as.matrix method and alike below).
as.vector: signature(x = "Vegsoup", mode = "missing"): is a shortcut to as.vector(as.matrix(x, typeof = mode), mode). Note, here the 'mode' argument has the meaning of the base R function and specifies the storage mode of the returned vector.

Together, indices and as.vector can be used to create a species matrix. See as.matrix.

7) Retrieve species matrix. In fact there are several ways of how to obtain the species matrix from an Vegsoup* object and all are based on the logic of object coercion. There are methods focused on a specific storage mode, as well, as a generic as.matrix coercion method. The following section outlines even more general index methods.

as.character: signature(x = "Vegsoup"): returns a matrix of mode "character" with species abundances in the data set's original scale.
as.logical: signature(x = "Vegsoup"): returns a matrix of mode "numeric" with zeros coding for species absences and ones for presences.
as.numeric: signature(x = "Vegsoup"): returns a matrix of mode "numeric" with species abundances recoded according to coverscale(obj).
as.matrix: signature(x = "Vegsoup"): retrieves a species matrices like those outlined above by setting the typeof argument specifying the mode of the returned matrix; can be one of "character", "numeric" or "logical". Use the additional argument mode with all four methods to get matrix transpositions. See as.matrix.

8) Retrieve dissimilarity/distance matrix.

as.dist: signature(m = "Vegsoup"): compute a distance matrix as specified by vegdist(obj). See as.dist
getDistconnected: signature(obj = "Vegsoup"): tests if dissimilarities/distances are connected.

9) Retrieve class slots. Methods to access or replace the 'species', 'sites' or 'taxonomy' slots are:

species: signature(obj = "Vegsoup"): returns slot, on object of class Species.
species<-: signature(obj = "Vegsoup", value = "Species"): assigns object of class Species to an existing Vegsoup* object. See species<-. signature(obj = "Vegsoup", value = "SpeciesTaxonomy"): assigns object of class "SpeciesTaxonomy" to an existing Vegsoup* object. Not implemented yet! See SpeciesTaxonomy.
sites: signature(obj = "Vegsoup"): returns slot, an object of class "data.frame". Note, the sites slot of Vegsoup objects is of class data.frame not Sites.
Sites<-: signature(obj = "Vegsoup", value = "data.frame"): The value object for the replacement function needs to have rownames matching rownames(obj).
Taxonomy: signature(obj = "Vegsoup"): returns slot, an object of class "data.frame", equaling an object of class Taxonomy.
Taxonomy<-: signature(obj = "Vegsoup", value = "SpeciesTaxonomy"): assign object of class "SpeciesTaxonomy" to an existing Vegsoup* object. Not implemented yet! See SpeciesTaxonomy

Methods to access or replace the 'Spatial*' slots are:

SpatialPointsVegsoup: signature(obj = "Vegsoup"): returns object of class SpatialPointsDataFrame.
SpatialPolygonsVegsoup: signature(obj = "Vegsoup"): returns object of class SpatialPolygonsDataFrame.
apriori: signature(obj = "Vegsoup"): returns a vector of a-priori group assignments. If not defined an "integer" vector of length equal to nrow(obj).

10) Names and species abbreviations.

dimnames: signature(x = "Vegsoup"): dimnames of the species matrix. See dimnames.
rownames: signature(x = "Vegsoup"): rownames of the species matrix, as well as of the sites data frame.
colnames: signature(x = "Vegsoup"): the column names of the species "matrix". See abbr.layer.
names: signature(x = "Vegsoup"): the column names of the sites "data.frame".
names<-: signature(x = "Vegsoup", value = "character"):
abbr: signature(obj = "Vegsoup"): abbreviations used to encode species.
abbr.layer: signature(obj = "Vegsoup"): abbreviations used to encode (pseudo-)species (layer replicates).
splitAbbr: signature(obj = "Vegsoup"): returns a data.frame. See splitAbbr.

11) Extract and replace.

[: signature(x = "Vegsoup", i = "ANY", j = "ANY"): provides all common indexing operations allowed for class "matrix".
[<-: signature(x = "Vegsoup", i = "ANY", j = "missing"): allows assignments to slot 'sites' . Note, this does not affect the species matrix.
$: signature(x = "Vegsoup"): access columns of sites data by name.
$<-: signature(x = "Vegsoup"): assign columns of sites data by name.

12) Row and column aggregation.

colSums: signature(x = "Vegsoup"): returns colSums(as.logical(obj)), hence does not take species abundance/cover values into consideration.
rowSums: signature(x = "Vegsoup"): returns rowSums(as.logical(obj)), same as above but for rows.
colMeans: signature(x = "Vegsoup"): returns colMeans(as.numeric(obj)) of species abundance/cover values.
rowMeans: signature(x = "Vegsoup"): returns rowMeans(as.numeric(obj)).
richness: signature(obj = "Vegsoup"): Conceptually similar to the methods outlined above, but tailored to respect the layer structure of an object in a special way. See richness for details.

13) Reorder and sample.

seriation: signature(obj = "Vegsoup"): modifies order as to reflect a vegetation table.
sample: signature(x = "Vegsoup"): random samples and permutations.

14) Plotting methods.

plot: signature(x = "Vegsoup", y = "missing"): a simple descriptive plot of the data set.
coldiss: signature(obj = "Vegsoup"): plots of the dissimilarity matrix.
map: signature(obj = "Vegsoup"): plots a plain map.

15) Spatial methods.

coordinates: signature(obj = "Vegsoup"): returns the a "matrix" of coordinates. See coordinates.
elevation: signature(obj = "Vegsoup"): queries elevation for plot coordinates from the SRTM3 data set.
quicklook: signature(obj = "Vegsoup"): open a map in browser window.

16) Summary methods.

summary: signature(object = "Vegsoup"): prints an summary.
head: signature(x = "Vegsoup"): prints the top rows of the species matrix.
tail: signature(x = "Vegsoup"): prints the bottom rows of the species matrix.
taxalist: signature(obj = "Vegsoup"): returns a complete list of species with corresponding abbreviations.

17) Coerce methods.

coerce: signature(from = "Vegsoup", to = "dist"): same as as.dist(obj) (see above). signature(from = "Vegsoup", to = "list"): returns objects all of class "data.frame" from slots 'species', 'sites' and 'taxonomy'. signature(from = "Vegsoup", to = "matrix"): same as as.matrix(obj) (see above). signature(from = "Vegsoup", to = "data.frame"): returns objects all of class "data.frame". See as.data.frame. signature(from = "Vegsoup", to = "data.list"): returns objects all of class "data.list". See as.data.list. signature(from = "Vegsoup", to = "dsparseMatrix"): returns objects all of class "dsparseMatrix". See as.matrix. signature(from = "Vegsoup", to = "sparseMatrix"): returns objects all of class "sparseMatrix". See as.matrix.

18) Combine objects.

bind: signature(... = "Vegsoup"): combine/merge objects.

1) Output methods.

KML: signature(obj = "Vegsoup"): writes a KML file for visualization in Google Earth.
write.verbatim: signature(obj = "Vegsoup"): writes the species matrix including header information to a plain text file.

1) Miscellaneous.

Indpower: signature(obj = "Vegsoup"): congruence between indicator and target species.
compspec: signature(obj = "Vegsoup"): compositional indicator species analysis.

Give notes!

Roland Kaiser

Species, Sites, Taxonomy, Vegsoup, instantsoup coenoflex