marmat {mefa} | R Documentation |
This is a utility function to calculate statistics on data matrices in objects of class 'xcount' and 'mefa'.
marmat(x, which = c("samples", "species"), method = c("abund", "occur"), group = NULL)
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:ncol(x)) depending on value of which .
The vector is treated as factor, to aggregate values of matrix x . |
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).
A result is a vector.
Peter Solymos, Solymos.Peter@aotk.szie.hu, http://www.univet.hu/users/psolymos/personal/
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))