| exclmf {mefa} | R Documentation |
Excludes species or samples in object of class 'xcount' or 'mefa'.
exclmf(xc, which = c("samples", "species"), excl, empty = FALSE)
xc |
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 is not "none"). |
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 samples are to be excluded, the
resulting empty columns for species will be removed, and vica versa. |
If species are excluded, some samples might have zero total count. In such cases,
it is advisable to use empty=TRUE.
Empty rows can be removed by which="species", excl=NULL and empty=FALSE.
A result is an object of class 'xcount' or 'mefa' depending on the input object.
If the resultant crosstable contains less than two rows/columns, an error message is given and there will be no output.
Peter Solymos, Solymos.Peter@aotk.szie.hu, http://www.univet.hu/users/psolymos/personal/
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)