add.attrib {mefa} | R Documentation |
The function adds attributes to an object ofclass 'mefa'.
add.attrib(mf, which = c("samples", "species"), attrib, index = 0)
mf |
a 'mefa' object. |
which |
attribute table within the 'mefa' object to be extended by new attributes, it can be the
"species" and "samples" attribute table. |
attrib |
name of the data frame containing new attributes. |
index |
column index of the data frame attrib containing new attributes, default (index = 0 ) it
refers to the rownames of the attribute table. |
A result is an object of class 'mefa' containing the original and the new attributes as well. Index column (index > 0
) from the new attributes table is removed, because it is a duplum.
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") sampletab1 <- as.data.frame(rbind( c("sample3", "bad"), c("sample1", "not-so-bad"), c("sample2", "good"), c("sample4", "very-bad"))) colnames(sampletab1) <- c("sample", "quality") sampletab2 <- as.data.frame(rbind( c("sample4", "debrecen", "nagyerdo", "bekasto", "2050-12-31", "bencike"), c("sample2", "pecs", "tettye", "mecsek", "1956-10-23", "barna"), c("sample1", "kiralyret", "bajdazoi", "bank", "2000-01-01", "XY"), c("sample3", "budapest", "pest", "rottenbiller", "2007-10-03", "SP"))) rownames(sampletab2)<-sampletab2[,1] colnames(sampletab2) <- c("sample", "locality1", "locality2", "locality3", "date", "collector") 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") xct <- xcount(sscount(ss, zc="zero.count")) xo1 <- xorder(xct, "samples", sampletab1, 1) xo2 <- xorder(xct, "species", spectab, 1) mf1 <- mefa(xct, xo1, xo2) (mf1a <- add.attrib(mf1, "samples", sampletab2)) mf2 <- mefa(xct, NULL, xo2) (mf2a <- add.attrib(mf2, "samples", sampletab2)) ### Example 2: field data of Villany Hills ## Not run: data(vtable, landsnail, vsample, vhabitat) vmf <- mefa( vt <- as.xcount(vtable, FALSE), xorder(vt, which="samples", vsample), xorder(vt, which="species", landsnail[,1:4], 2) ) extra <- landsnail[,c(2, 5:8)][order(rnorm(nrow(landsnail))),] vmf2 <- add.attrib(vmf, which="species", extra, 1) vmf2 ## End(Not run)