Cross Tabulate an Object of Class 'stcs'

The function makes cross tabulation of an object of class 'stcs'. Similar to the table function but handles specialities 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.

Usage

mefaCrosstab(x, segment = FALSE, nested = FALSE, drop.zero = FALSE)

Arguments

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).

Details

The cross tabulation of an object of class 'stcs' is made by the function xtabs, whic accepts non-integer values too.

Value

It returs a matrix if segment = FALSE or a list with matrices for the segments if segment = TRUE.

References

S\'olymos P. (2008) mefa: an R package for handling and reporting count data. Community Ecology 9, 125--127.

S\'olymos P. (2009) Processing ecological data in R with the mefa package. Journal of Statistical Software 29(8), 1--28. doi:10.18637/jss.v029.i08

http://mefa.r-forge.r-project.org/

Author

P\'eter S\'olymos, solymos@ualberta.ca

Examples

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)
#>     taxa
#> samp  e f g
#>    A  3 0 0
#>    B 10 3 0
#>    C  0 0 4
#>    D  0 0 0
mefaCrosstab(y, segment = TRUE)
#> $h
#>     taxa
#> samp  e f g
#>    A  1 0 0
#>    B 10 0 0
#>    C  0 0 4
#>    D  0 0 0
#> 
#> $i
#>     taxa
#> samp e f g
#>    A 2 0 0
#>    B 0 3 0
#>    C 0 0 0
#>    D 0 0 0
#> 
mefaCrosstab(y, segment = TRUE, nested = TRUE)
#> $h
#>     taxa
#> samp  e f g
#>    A  1 0 0
#>    B 10 0 0
#>    C  0 0 4
#>    D  0 0 0
#> 
#> $`h-i`
#>     taxa
#> samp  e f g
#>    A  3 0 0
#>    B 10 3 0
#>    C  0 0 4
#>    D  0 0 0
#> 
## Examples for non-integer data
y[1:5, 3] <- y[1:5, 3] + 0.123
mefaCrosstab(y)
#>     taxa
#> samp      e     f     g
#>    A  3.246 0.000 0.000
#>    B 10.123 3.123 0.000
#>    C  0.000 0.000 4.123
#>    D  0.000 0.000 0.000
mefaCrosstab(y, segment = TRUE)
#> $h
#>     taxa
#> samp      e f     g
#>    A  1.123 0 0.000
#>    B 10.123 0 0.000
#>    C  0.000 0 4.123
#>    D  0.000 0 0.000
#> 
#> $i
#>     taxa
#> samp     e     f g
#>    A 2.123 0.000 0
#>    B 0.000 3.123 0
#>    C 0.000 0.000 0
#>    D 0.000 0.000 0
#>