melt.mefa: Melt (Convert) an Object of Class 'mefa' Into 'stcs'
In mefa: Multivariate Data Handling in Ecology and Biogeography

Description Usage Arguments Details Value Author(s) References Examples

The function converts a wide formatted 'mefa' object into a long formatted 'stcs' object. The resulting segment column can take various formats.

melt(x, ...)
## S3 method for class 'mefa'
melt(x, segm.var = NULL, by.samp = TRUE,
raw.out = FALSE, drop.zero = FALSE, ...)

`x`	an object of class 'mefa'.
`segm.var`	`NULL` (default) or column indices of samples (if `by.samp = TRUE`) or taxa tables (if `by.samp = FALSE`). If it refers to more than one column, their interaction is taken. If `NULL`, the resulting segment column is filled with `"undefined"`.
`by.samp`	logical, if `TRUE` (default) `segm.var` is taken from the samples table (`x$samp`), if `FALSE` `segm.var` is taken from the taxa table (`x$taxa`).
`raw.out`	logical, whether the result should contain all the zeros that is in the crosstabulated (wide) matrix (`TRUE`) or not (`FALSE`, default). Removing the zeros is straightforward for sparse matrices. But empty samples can be retained if `drop.zero = FALSE`.
`drop.zero`	logical, whether samples with zero total count should be leaved out (`TRUE`) or not (`FALSE`, default).
`...`	other arguments passed to the function `stcs`.

If a 'mefa' objet has original segments and segm.var = NULL, the function returns original segments. In this case, the raw.out = TRUE cannot be applied (because segments have different zero samples, so the option is meaningless). If the 'mefa' object contains only a data matrix without dimnames, rows and columns are numbered before melting.

Besides the goal to convert from wide format to long format, this 'mefa' specific implementation is also useful, if a segment is not coded along with the long formatted database, but can be found in a linked table of samples or species. In this way, a 'mefa' object with new segments can be defined easily.

If melting is done with a vector that is not part of the tables inside the 'mefa' object, it must have a class attribute to be recognised, use e.g. the as.factor function (see 'Examples').

An object of class 'stsc' if raw = FALSE, pure 'data.frame' otherwise (because the zero count flag cannot be applied).

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

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/

data(dol.count, dol.samp, dol.taxa)
x <- mefa(stcs(dol.count), dol.samp, dol.taxa)
## Long format with original segments
melt(x)
## Long format with undefined segment
melt(as.mefa(x, segment = FALSE))
## These two are identical
melt(x, "microhab")
melt(x, x$samp$microhab) ## this is a factor
## Using a simple vector as factor
melt(x, as.factor(rbinom(dim(x)[1], 1, 0.5)))
## Interaction
melt(x, c("method", "microhab"))
## From taxa table
melt(x, "familia", by.samp = FALSE)
## Example for non-integer data
y <- x$xtab
y[y > 0] <-  y[y > 0] + 0.123
z <- mefa(y)
melt(z)