## Not run:
# #### H3N2 ####
# ## LOAD DATA
# data(H3N2)
# H3N2
#
# ## set population to yearly epidemics
# pop(H3N2) <- factor(H3N2$other$epid)
#
#
#
# ## PERFORM DAPC - USE POPULATIONS AS CLUSTERS
# ## to reproduce exactly analyses from the paper, use "n.pca=1000"
# dapc1 <- dapc(H3N2, all.contrib=TRUE, scale=FALSE, n.pca=150, n.da=5)
# dapc1
#
# ## (see ?dapc for details about the output)
#
#
# ## SCREEPLOT OF EIGENVALUES
# barplot(dapc1$eig, main="H3N2 - DAPC eigenvalues")
#
#
# ## SCATTERPLOT (axes 1-2)
# scatter(dapc1, posi.da="topleft", cstar=FALSE, cex=2, pch=17:22,
# solid=.5, bg="white")
#
#
#
#
# #### usflu.fasta ####
# myPath <- system.file("files/usflu.fasta",package="adegenet")
# myPath
#
# ## extract SNPs from alignments using fasta2genlight
# ## see ?fasta2genlight for more details
# obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time
# obj
# ## End(Not run)
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