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. The function name 'stcs' refers to first letters of column names of the resulting object: samples, taxa, counts, segments.
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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 (either integer or non-integer values can be supplied), and segment if character or factor. If 4 columns are provided, those are assumed to be in the samples, taxa, count, segment order.
logical, whether the object should be (
logical, whether samples with zero total count should be left out (
character, value in the
an object of class 'stcs'.
further arguments passed to the function
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, and this is only for integer data), or alternatively see the
mefaCrosstab functions (these accepts non-integer data). For subsetting, simply use extraction methods available for data frames (
The summary contains statistics calculated after coercing the object into the class 'mefa'.
Methods for extracting, subsetting are the same as for data frame objects. Plotting 'stcs' objects are discussed elsewhere (see links in 'See also' section).
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 its own methods (i.e.
plot), but also has a
data.frame class attribute. Thus other methods that available for data frames are applicable to an object of class 'stcs' (e.g.
stcs function nearly equivalent to the
sscount function in older (< 2.0) versions of the mefa package.
P\'eter S\'olymos, [email protected]
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. http://www.jstatsoft.org/v29/i08/
as.stcs for coercion methods.
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## 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(dol.count) dol <- stcs(dol.count) dol plot(dol)
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