mefa (version 1.1-4)

marmat: Marginal Statistics for Matrices

Description

This is a utility function to calculate statistics on data matrices in objects of class 'xcount' and 'mefa'.

Usage

marmat(x, which = c("samples", "species"), method = c("abund", "occur"), group = NULL)

Arguments

x

a matrix containing data.

which

"samples" indicates rows (default), "species" indicates columns, on which the function will be applied over.

method

sets method to use, "abund" refers to abundance data (use data in x as is), "occur" (occurence) refers to column/row sums in a presence/absence (binary) matrix.

group

NULL (default) or a vector with length sames as the number of rows (for which="samples"), or columns (for which="samples"). If NULL it takes the value c(1:nrow(x)) or c(1:n

Value

• A result is a vector.

Details

This function can be used on eg. data tables of count or abundance matrices to calculate number of individuals or species richness (method="occur") within samples (which="samples") or groups of samples (which="samples", and group differs from the default), or abundance (method="abund") or number of occurences (method="occur") of species (which="species") or species groups (which="species", and group differs from the default).

Examples

x <- matrix(data = rpois(8*4, 1), nrow = 8, ncol = 4)
rownames(x) <- letters[1:8]
colnames(x) <- LETTERS[1:4]

marmat(x, "samples", "abund")
marmat(x, "samples", "abund", group=c(1,1,2,2,3,3,4,4))
marmat(x, "samples", "occur")
marmat(x, "samples", "occur", group=c(1,1,2,2,3,3,4,4))

marmat(x, "species", "abund")
marmat(x, "species", "abund", group=c(1,1,2,2))
marmat(x, "species", "occur")
marmat(x, "species", "occur", group=c(1,1,2,2))