mefa (version 1.1-4)

add.attrib: Add Attributes to Object of Class 'mefa'

Description

The function adds attributes to an object ofclass 'mefa'.

Usage

add.attrib(mf, which = c("samples", "species"), attrib, index = 0)

Arguments

mf

a 'mefa' object.

which

attribute table within the 'mefa' object to be extended by new attributes, it can be the "species" and "samples" attribute table.

attrib

name of the data frame containing new attributes.

index

column index of the data frame attrib containing new attributes, default (index = 0) it refers to the rownames of the attribute table.

Value

• A result is an object of class 'mefa' containing the original and the new attributes as well. Index column (index > 0) from the new attributes table is removed, because it is a duplum.

See Also

mefa

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")

sampletab1 <- as.data.frame(rbind(
	c("sample3", "bad"),
	c("sample1", "not-so-bad"),
	c("sample2", "good"),
	c("sample4", "very-bad")))
colnames(sampletab1) <- c("sample", "quality")

sampletab2 <- as.data.frame(rbind(
	c("sample4", "debrecen", "nagyerdo", "bekasto", "2050-12-31", "bencike"),
	c("sample2", "pecs", "tettye", "mecsek", "1956-10-23", "barna"),
	c("sample1", "kiralyret", "bajdazoi", "bank", "2000-01-01", "XY"),
	c("sample3", "budapest", "pest", "rottenbiller", "2007-10-03", "SP")))
rownames(sampletab2)<-sampletab2[,1]
colnames(sampletab2) <- c("sample", "locality1", "locality2", "locality3", "date", "collector")

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")

xct <- xcount(sscount(ss, zc="zero.count"))
xo1 <- xorder(xct, "samples", sampletab1, 1)
xo2 <- xorder(xct, "species", spectab, 1)

mf1 <- mefa(xct, xo1, xo2)

(mf1a <- add.attrib(mf1, "samples", sampletab2))

mf2 <- mefa(xct, NULL, xo2)
(mf2a <- add.attrib(mf2, "samples", sampletab2))

### Example 2: field data of Villany Hills

data(vtable, landsnail, vsample, vhabitat)

vmf <- mefa(
vt <- as.xcount(vtable, FALSE), 
xorder(vt, which="samples", vsample),
xorder(vt, which="species", landsnail[,1:4], 2)
)

extra <- landsnail[,c(2, 5:8)][order(rnorm(nrow(landsnail))),]

vmf2 <- add.attrib(vmf, which="species", extra, 1)
vmf2