Trying to follow the instructions here:
I want to read in my phylogenetic tree with the 'treeio' package. And get all the values associated with the nodes. Or any other package for that matter.
After having installed 'ips' and 'treeio' and the 'ape' package, and I have set a path to my working directory.
I tried this:
phyA <- read.beast("bk98_01_11_A7.tre", digits = NULL)
But this did not work.
It returned this error:
Error in (i2 + 1):end : argument of length 0
I then tried installing the "OutbreakTools" package.
And I then tried this:
phyA <- read.annotated.nexus("bk98_01_11_A7.tre")
this worked fine. But when I then examining a node (e.g. node number 69 ) in my tree object:
phy <- phyA phy$annotations[]$
I get :
But looking at this value at this node (69) in FigTree I can see the values should be :
3.813 and 18.423
I also had a look here:
But could not get any of the suggested approaches to work.
The tree I am using can be reached here.
My input tree might be wrong. But I have no idea to how the file should be instead. Thanks in advance for any help on this.