marmat {mefa}R Documentation

Computes Marginal Sums of Presence Absence or Abundance 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.
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.
which "samples" indicates rows (default), "species" indicates columns, on which the function will be applied over.
group NULL (default) or a vector with length sames as the number of rows (for which="samples"), or columns (for which="samples"). I NULL it takes the value c(1:nrow(x)) or c(1:ncol(x)) depending on value of which. It is treated as factor, to aggregate values of matrix x.

Details

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

Value

A result is a vector.

Author(s)

Peter Solymos, Solymos.Peter@aotk.szie.hu, http://www.univet.hu/users/psolymos/personal/

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))

[Package mefa version 1.1-0 Index]