I vaguely remember similar issues in my own simulator long ago, and the solution was:
tr2 = read.tree(file="", text=write.tree(simtree, file="")) Cheers! Nick On Wed, Nov 20, 2024 at 3:12 PM Alex Skeels <[email protected]> wrote: > 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/[email protected]/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
