xorder {mefa} | R Documentation |
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
.
xorder(xc, which = c("samples", "species"), attrib, index = 1)
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 it is the first column of data frame attrib . |
A result is an object of class 'xorder'.
which |
the value of the which argument, either "samples" or "species" . |
check.setrel |
set.relation value of function check.attrib . |
check.dupl |
duplicate value of function check.attrib . |
data |
data frame, ordered and subsetted according to the 'xcount' object. |
Peter Solymos, Solymos.Peter@aotk.szie.hu, http://www.univet.hu/users/psolymos/personal/
### 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 ## Not run: data(vtable, vsample, landsnail) vt <- as.xcount(vtable, FALSE) spec <- xorder(vt, which="species", landsnail, 2) spec sampl <- xorder(vt, which="samples", vsample) sampl ## End(Not run)