mvabund: Multivariate Abundance Data Objects

In mvabund: Statistical Methods for Analysing Multivariate Abundance Data

Multivariate Abundance Data Objects

Description

mvabund creates an mvabund object.
as.mvabund attempts to turn its argument into an mvabund object.
is.mvabund tests if the argument is an mvabund object.
mvabund is a class of objects for which special-purpose plotting and regression functions have been written in the mvabund-package. The above are useful preliminary functions before analysing data using the special-purpose functions. These new functions were written specially for the analysis of multivariate abundance data in ecology, hence the title 'mvabund'.

Usage

mvabund( ... , row.names=NULL, check.rows=FALSE, check.names=TRUE,
  var.names=NULL, neg=FALSE, na.rm=FALSE )
  
as.mvabund(x)

is.mvabund(x)

Arguments

...	these arguments are of either the form value or tag = value. Component names are created based on the tag (if present) or the deparsed argument itself.
row.names	NULL or a single integer or character string specifying a column to be used as row names, or a character or integer vector giving the row names for the mvabund object.
check.rows	if TRUE then the rows are checked for consistency of length and names.
check.names	logical. If TRUE then the names of the variables are checked to ensure that they are syntactically valid variable names and are not duplicated. If necessary they are adjusted (by make.names) so that they are.
var.names	NULL or a character vector giving the column names for the mvabund object.
neg	character. If FALSE negative values will cause an error message.
na.rm	logical, whether missing values should be removed.
x	an R object.

Details

It is desirable to convert abundance data to mvabund objects, to allow automatic use of all methods for mvabund objects, for example the provided methods for plotting, linear and generalised linear model-fitting and inference.

Some more technical details:
mvabund objects always have two dimensions.
mvabund converts its arguments into an mvabund object. The supplied argument can be a matrix, data frame, a list of vectors, or several vectors as separate arguments.

If elements of the created mvabund object are not numeric, a warning will be printed.

If row.names are not supplied, the row names of the mvabund object will be NULL. If the length of row.names does not match the number of rows or there are duplicates, an error message will result.

Value

mvabund and as.mvabund returns an mvabund object.
is.mvabund returns TRUE if x is a matrix and FALSE otherwise.

Author(s)

Ulrike Naumann and David Warton <[e-mail]>.

See Also

unabund, mvformula, plot.mvabund, Also see the mvabund-package.

Examples

data(solberg) 

## Create an mvabund object:
solbergdat <- mvabund(solberg$abund)

## Turn solberg$abund into an mvabund object and store as solbergdat:
solbergdat <- as.mvabund(solberg$abund)

## Check if solbergdat  is an mvabund object:
is.mvabund(solbergdat)

mvabund documentation built on March 18, 2022, 7:25 p.m.