Consider the following dataset:
fictional.df <- data.frame(L1 = c(0,0,0,0,0,0,0,0),
L2 = c(0,1,0,0,0,1,1,0),
L3 = c(1,1,0,1,1,1,1,1),
L4=c(0,0,1,1,0,0,0,0))
I
- converted this to a
phyDatobject and then - created a pairwise distance matrix as follows:
fictional.phydat <- as.phyDat(fictional.df,
type="USER",levels=c("1","0"),
names=names(fictional.df))
fictional.hamming <- dist.hamming(fictional.phydat)
- From this distance matrix, I then estimated a UPGMA tree:
fictional.upgma <- upgma(fictional.hamming)
- I then created bootstrap datasets:
set.seed(187)
fictional.upgma.bs <- bootstrap.phyDat(fictional.phydat, FUN =
function(xx) upgma(dist.hamming(xx)), bs=100)
- I then calculated the proportion of partitions in the bootstrap set:
upgma.bs.part <- prop.part(fictional.upgma.bs)
- So far so good. Here is where I would appreciate some help. When I call the function
prop.clades, I do not understand the result:
prop.clades(fictional.upgma,fictional.upgma.bs)
[1] 100 NA 71
Question Why does this function return NA when there is evidence for that clade in the set of bootstrap trees?
A second question:
prop.clades(fictional.upgma,part=upgma.bs.part)
[1] 100 49 112
If there are only 100 bootstrap samples, why is the value for the final clade 112?