exclmf: Exclude Species or Samples in Object of Class 'xcount' or 'mefa'

Description

Excludes species or samples in object of class 'xcount' or 'mefa'.

Usage

exclmf(xc, which = c("samples", "species"), excl, empty = FALSE)

Arguments

an object of class 'xcount' or 'mefa' to be used.

which

switch between rows ("samples") and columns ("species") to be excluded.

excl

list of rows/columns (samples/species) to be excluded (according to which argument). If excl=NULL, nothing will be excluded (only useful when empty = TRUE).

empty

logical, if FALSE (default), rows with zero sum will be left intact, TRUE means that exclusion of empty rows/columns will be executed according to sums of the opposite margin of the sample-species matrix, ie. if sampl

Value

A result is an object of class 'xcount' or 'mefa' depending on the class of the input object.

Details

If species are excluded, some samples might have zero total count. In such cases, empty=TRUE can be used to get rid of these null samples. Empty rows can be removed by which="species", excl=NULL and empty=FALSE.

Examples

Run this code

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)

exclmf(xct, "samples", NULL, FALSE)
exclmf(xct, "samples", 3, FALSE)
exclmf(xct, "samples", 3, TRUE)
exclmf(xct, "samples", c(1:2), FALSE)

exclmf(xct, "species", NULL, TRUE) ## use to remove empty rows
exclmf(xct, "species", 1, FALSE)
exclmf(xct, "species", 1, TRUE)

exclmf(mf1, "samples", 3, FALSE)
exclmf(mf1, "samples", 3, TRUE)