mefa {mefa} | R Documentation |
Makes and object of class 'mefa' from az 'xcont' and sample and species attribute 'xorder' objects.
mefa(xc, xorder.samples, xorder.species)
xc |
object of class 'xcount'. |
xorder.samples |
object of class 'xorder' for sample attributes. |
xorder.species |
object of class 'xorder' for species attributes. |
A result is an object of class 'mefa'.
segment |
segment of the 'xcount' object. |
xcount |
count data from the 'xcount' object |
sample.attr |
data frame containing data of 'xorder' object containing sample attributes. |
species.attr |
data frame containing data of 'xorder' object containing species attributes. |
nsamples |
number of samples. |
nspecies |
number of species. |
totalcount |
total number of counts in xcount . |
nsample.attr |
number of sample attribute columns in sample.attr . |
nspecies.attr |
number of species attribute columns in species.attr . |
Peter Solymos, Solymos.Peter@aotk.szie.hu, http://www.univet.hu/users/psolymos/personal/
check.attrib
, sscount
, xcount
, xorder
### 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, zc="zero.count")) xo1 <- xorder(xct, "samples", sampletab, 1) xo2 <- xorder(xct, "species", spectab, 1) mf1 <- mefa (xct, xo1, xo2) mf1 mf2 <- mefa(xcount(sscount(ss, zc="zero.count"), 2), xo1, xo2) mf2 ### Example 2: field data of Villany Hills ## Not run: data(landsnail, vsample, vtable) vt <- as.xcount(vtable, FALSE) spec <- xorder(vt, which="species", landsnail, 2) sampl <- xorder(vt, which="samples", vsample) vmf <- mefa(vt, sampl, spec) vmf ### Example 3: field data of the dolina data(dol.count, dol.sample, landsnail) dmf <- mefa( dxc <- xcount(sscount(fill.count(dol.count), zc="zero.count")), xorder(dxc, which="samples", dol.sample), xorder(dxc, which="species", landsnail, 2) ) dmf ## End(Not run)