stcs {mefa} | R Documentation |
This function creates object of class 'stcs' from a data frame. This is the primary format for long (database style) data sets in the mefa package. The 'stcs' object can be converted into an object of class 'mefa' with the function mefa
stcs(xtab, expand = FALSE, drop.zero = FALSE, zero.pseudo = "zero.pseudo") ## S3 method for class 'stcs': is(x) ## S3 method for class 'stcs': as(x, ...)
xtab |
a data frame with 2-4 columns. If 2 columns are provided, it is assumed that first column contains sample, while second taxa names. If 3 columns are provided, the first two is treated as sample and taxa names, while the third is treated as count if numeric, and segment if character or factor. If 4 columns are provided, those are assumed to be in the samples, taxa, count, segment order. |
expand |
logical, whether the object should be (TRUE ) expanded (via the function inflate ) or not (FALSE , default). If expanded, each rows correspond to one individual observation (value of the count column is 1) or a zero sample. |
drop.zero |
logical, whether samples with zero total count should be left out (TRUE ) or not (FALSE , default). |
zero.pseudo |
character, value in the taxa column that indicates zero samples. |
x |
an object of class 'stcs'. |
... |
further arguments passed to the function stcs . |
If the data are in a long (database style) format, the stcs
function prepares the ground for the mefa
function to make the cross tabulation. But if only a crosstabulated matrix is needed, the table
function can be applies as well (in this case be sure to set expand = TRUE
). For subsetting, simply use extraction methods available for data frames ([.data.frame
).
Returns an object of class 'stcs' with 4 columns. The column names are converted consistently into samp
for samples, taxa
for taxa names, count
for counts and segm
for segment names.
The class has some own methods (i.e. is
and as
), but also has a data.frame
class attribute. Thus all methods available for data frames are applicable to an object of class 'stcs' (e.g. summary
, str
).
The stcs
function nearly equivalent to the sscount
function in older (< 2.0) versions of the mefa package.
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/
data.frame
, summary.data.frame
, str
, table
## General long format data x <- data.frame( sample = paste("Sample", c(1,1,2,2,3,4), sep="."), species = c(paste("Species", c(1,1,1,2,3), sep="."), "zero.pseudo"), count = c(1,2,10,3,4,0), segment = letters[c(6,13,6,13,6,6)]) x ## Long format as stcs y <- stcs(x) y ## Methods as.stcs(x) is(y, "stcs") is(y, "data.frame") ## Effects of arguments stcs(x, expand = TRUE) stcs(x, drop.zero = TRUE) stcs(x, zero.pseudo = "pseudo.secies") ## Input options stcs(x[,1:2]) stcs(x[,1:3]) stcs(x[,c(1:2,4)]) ## The DOLINA dataset data(DOLINAcounts) dol <- stcs(DOLINAcounts) dol