mefa (version 1.1-4)

xorder: Make Object of Class 'xorder'

Description

The function makes an object of class 'xorder' from an attribute table (data frame) based on comparison with an 'xcount' object. Data frame subsetting is made according to results of function check.attrib.

Usage

xorder(xc, which = c("samples", "species"), attrib, index = 0)

## S3 method for class 'xorder':
print(x, \dots)

Arguments

xc

an object of class 'xcount'.

which

switch for rows ("samples") or columns ("species") of the 'xcount' object to be compared according to index.

attrib

data frame to be checked.

index

column identifier within attrib to be compared according to row/column names (as sample/species identifiers) of the 'xcount' object according to value of which. By default, index = 0, and rownames are taken as identifi

x

an object of class 'xorder'.

...

other arguments.

Value

• A result is an object of class 'xorder'.
• data
  data frame, ordered and subsetted according to the 'xcount' object.
• call
  returns the call.
• which
  the value of the which argument, either "samples" or "species".
• check.setrel
  set.relation value of function check.attrib.
• na
  indicates the number of NA values in attrib.

See Also

check.attrib, mefa, xcount

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, "zero.count"))

xo1 <- xorder(xct, "samples", sampletab, 1)
xo2 <- xorder(xct, "species", spectab, 1)

### Example 2: field data of Villany Hills

data(vtable, vsample, landsnail)

vt <- as.xcount(vtable, FALSE)

spec <- xorder(vt, which="species", landsnail, 2)
spec

sampl <- xorder(vt, which="samples", vsample, 1)
sampl