mefa (version 1.1-4)

check.attrib: Check Consistency of 'xcount' Object and Attribute Table

Description

This function checks consistency of an object of class 'xcount' and an attribute table (data frame) by comparing row/column names (as sample/species identifiers) and values in an index column of the data frame.

Usage

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

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. NA values are counted.

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 take

Value

• call
  returns the call.
• set.relation
  "equal" means the two sets (row/column names of the 'xcount' object and elements in the index column) are equal, "inclusion" means the two sets are inclusive and no missing elements found, "intersect" means the two sets intersect (required elements are listed in missing), "separate" means the two sets have no common elements (required elements are listed in missing).
• duplicate
  a list of duplicate elements or NULL.
• missing
  a list of missing elements or NULL.
• na
  indicates the number of NA values found in attrib.

See Also

mefa, 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))

check.attrib(xct, "samples", sampletab, 1)
check.attrib(xct, "species", spectab, 1)
check.attrib(xct, "species", spectab, 2)
check.attrib(xct, "species", spectab[2:5,], 1)
check.attrib(xct, "species", spectab[4:5,], 1)

### Example 2: field data of Villany Hills

data(vtable, vsample, landsnail)

vt <- as.xcount(vtable, FALSE)

check.attrib(vt, which="species", landsnail, 2)
check.attrib(vt, which="samples", vsample, 1)