Hi everyone,
I have a problem that I've been stuck on for a bit. I am running a custom
simulation which keeps track of species divergences in an edge table
containing parent, descendent, and branch length information. Because it is
a forward-in-time sim it starts labelling nodes at "1" which is different
to how nodes are labelled in ape.
This is giving me problems reconstructing a tree from this table as I get
the Error in plot.phylo(tree) : tree badly conformed; cannot plot. Check
the edge matrix." when using my numbering system. It's not super intuitive
to know exactly what ape is expecting here and I'm wondering if anyone
knows and whether there's a straight forward way to convert to that format?
Here's a reproducible example of what I'm talking about. Any ideas how to
resolve this?
library(ape)
# set up an edgetable
edgetable <- data.frame(parent=c(0, 1, 1, 3, 3, 4, 5),
node=c(1,2,3,4,5,6,7), brlen=c(0.7, 5.6, 4.9, 0.6, 0.7, 0.1, 0.1))
# get the tips "nodes"
terminal_branches <- edgetable$node[which(edgetable$node %in%
edgetable$parent)]
# create list with necessary ingredients
tree <- list(edge=edgetable[,c("parent", "node")],
edge.length=edgetable[,"brlen"],
tip.label = paste0("species_", terminal_branches),
Nnode = length(terminal_branches)-1)
# turn list into phylo
class(tree) <- "phylo"
# ok looks good
tree
# plot
plot(tree)
# "Error in plot.phylo(tree) : tree badly conformed; cannot plot. Check the
edge matrix."
Thanks in advance!!
Cheers,
Alex Skeels
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