mefaCrosstab {mefa} | R Documentation |
The function makes cross tabulation of an object of class 'stcs'. Similar to the table
function but handles specialties of the 'stcs' object class (i.e. removes 'pseudo species' created to indicate empty samples). This is used internally by the function mefa
to make 3 dimensional representation of the data.
mefaCrosstab(x, segment = FALSE, nested = FALSE, drop.zero = FALSE)
x |
an object of class 'stcs'. |
segment |
logical, if TRUE , the crosstabulation is made in 2 dimensions by the samp (sample) and taxa columns of the x . Otherwise, crosstabulation is made in 3 dimensions by the samp , taxa and segm (segment) columns. |
nested |
logical, if FALSE count values of each segments are independent, if TRUE crosstabulated matrices are summed up in a nested fashion from segment level 1 to the number of segments (it is indicated in the segment levels as well). |
drop.zero |
argument passed to the function stcs , indicating whether empty samples (with zero sum) should be removed prior to cross tabulation (TRUE ), or not (FALSE ). |
The cross tabulation of an object of class 'stcs' is made by the function xtabs
, whic accepts non-integer values too.
It returs a matrix if segment = FALSE
or a list with matrices for the segments if segment = TRUE
.
Péter Sólymos, solymos@ualberta.ca
Sólymos P. 2008. mefa: an R package for handling and reporting count data. Community Ecology 9, 125–127.
http://mefa.r-forge.r-project.org/
x <- data.frame(sample = LETTERS[c(1,1,2,2,3,4)], species = c(letters[c(5,5,5,6,7)], "zero.pseudo"), count = c(1,2,10,3,4,0), segment = letters[c(8,9,8,9,8,8)]) y <- stcs(x) mefaCrosstab(y) mefaCrosstab(y, segment = TRUE) mefaCrosstab(y, segment = TRUE, nested = TRUE) ## Examples for non-integer data y[1:5, 3] <- y[1:5, 3] + 0.123 mefaCrosstab(y) mefaCrosstab(y, segment = TRUE)