# NOT RUN {
# }
# NOT RUN {
set.seed(23235)
ss <- TRUE # sample(1:150, 10 )
hc1 <- hclust(dist(iris[ss,-5]), "com")
hc2 <- hclust(dist(iris[ss,-5]), "single")
# tree1 <- as.treerogram(hc1)
# tree2 <- as.treerogram(hc2)
# cutree(tree1)
Bk_plot(hc1, hc2, k = 2:20, xlim = c(2,149))
Bk_plot(hc1, hc2)
Bk_plot(hc1, hc2, k = 3)
Bk_plot(hc1, hc2, k = 3:10)
Bk_plot(hc1, hc2)
Bk_plot(hc1, hc2,p.adjust.methods="bonferroni") # higher rejection lines
# this one can take a bit of time:
Bk_plot(hc1, hc2, rejection_line_permutation=TRUE,
k_permutation = c(2,4,6,8,10,20,30,40,50), R= 100)
# we can see that the permutation line is VERY close to the asymptotic line.
# This is great since it means one can often use the asymptotic results
# Without having to do many simulations.
# works just as well for dendrograms:
dend1 <- as.dendrogram(hc1)
dend2 <- as.dendrogram(hc2)
Bk_plot(dend1, dend2, k = 2:3, try_cutree_hclust = FALSE) # slower than hclust, but works...
Bk_plot(hc1, dend2, k = 2:3, try_cutree_hclust = FALSE) # slower than hclust, but works...
Bk_plot(dend1, dend1, k = 2:3, try_cutree_hclust = TRUE) # slower than hclust, but works...
Bk_plot(hc1, hc1, k = 2:3) # slower than hclust, but works...
# for some reason it can't turn dend2 back to hclust :(
a= Bk_plot(hc1, hc2, k = 2:3, try_cutree_hclust = TRUE) # slower than hclust, but works...
hc1_mixed <- as.hclust(sample(as.dendrogram(hc1)))
Bk_plot(tree1=hc1, tree2=hc1_mixed,
add_E=FALSE,
rejection_line_permutation=TRUE, k_permutation = c(2,4,6,8,10,20,30,40,50), R= 100)
# }
Run the code above in your browser using DataLab