mefa (version 3.1-0)

stcs: Create an Object of Class 'stcs'

Description

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, sebments.

Usage

stcs(dframe, expand = FALSE, drop.zero = FALSE, zero.pseudo = "zero.pseudo")
## S3 method for class 'stcs':
is(x)
## S3 method for class 'stcs':
summary(object, \ldots)

Arguments

dframe

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 numeri

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

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. If it is a vector of length 2, first element is used for taxa names, second for segment names to indicate zero samples.

x, object

an object of class 'stcs'.

...

further arguments passed to the function stcs.

encoding

UTF-8

Details

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 xtabs or mefaCrosstab functions (these accepts non-integer data). For subsetting, simply use extraction methods available for data frames (count, census.

Examples

## 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)