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 = 0) ## S3 method for class 'xorder': print(x, ...)
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 identifiers. |
x |
an object of class 'xorder'. |
... |
other arguments. |
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 . |
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, 1) sampl ## End(Not run)