mefa {mefa}R Documentation

Makes Object of Class 'mefa'

Description

Makes and object of class 'mefa' from az 'xcont' and sample and species attribute 'xorder' objects.

Usage

mefa(xc, xorder.samples, xorder.species)

Arguments

xc object of class 'xcount'.
xorder.samples object of class 'xorder' for sample attributes.
xorder.species object of class 'xorder' for species attributes.

Value

A result is an object of class 'mefa'.

segment segment of the 'xcount' object.
xcount count data from the 'xcount' object
sample.attr data frame containing data of 'xorder' object containing sample attributes.
species.attr data frame containing data of 'xorder' object containing species attributes.
nsamples number of samples.
nspecies number of species.
totalcount total number of counts in xcount.
nsample.attr number of sample attribute columns in sample.attr.
nspecies.attr number of species attribute columns in species.attr.

Author(s)

Peter Solymos, Solymos.Peter@aotk.szie.hu, http://www.univet.hu/users/psolymos/personal/

See Also

check.attrib, sscount, xcount, xorder

Examples

### Example 1: simple atrificial data

ss <- data.frame(
cbind(
c("sample1","sample1","sample2","sample2","sample3","sample4"),
c("species1","species1","species1","species2","species3","zero.count"),
c("male","female","male","female","male","male")
),
c(1, 2, 10, 3, 4, 1)
)
colnames(ss) <- c("sample.id", "species.id", "gender", "catch")

spectab <- as.data.frame(rbind(
        c("species3", "family1", "1"),
        c("species2", "family2", "5"),
        c("species1", "family1", "2"),
        c("species5", "family2", "1"),
        c("species4", "family1", "10")
))
colnames(spectab) <- c("species", "taxonomy", "size")

sampletab <- as.data.frame(rbind(
        c("sample3", "bad"),
        c("sample1", "good"),
        c("sample2", "good"),
        c("sample4", "bad")))
colnames(sampletab) <- c("sample", "quality")

xct <- xcount(sscount(ss, zc="zero.count"))
xo1 <- xorder(xct, "samples", sampletab, 1)
xo2 <- xorder(xct, "species", spectab, 1)

mf1 <- mefa (xct, xo1, xo2)
mf1

mf2 <- mefa(xcount(sscount(ss, zc="zero.count"), 2), xo1, xo2)
mf2

### Example 2: field data of Villany Hills

## Not run: 
data(landsnail, vsample, vtable)

vt <- as.xcount(vtable, FALSE)
spec <- xorder(vt, which="species", landsnail, 2)
sampl <- xorder(vt, which="samples", vsample)

vmf <- mefa(vt, sampl, spec)
vmf

### Example 3: field data of the dolina

data(dol.count, dol.sample, landsnail)

dmf <- mefa(
dxc <- xcount(sscount(fill.count(dol.count), zc="zero.count")),
xorder(dxc, which="samples", dol.sample),
xorder(dxc, which="species", landsnail, 2)
)

dmf
## End(Not run)
[Package mefa version 1.0 Index]