Hi Fan,
The code of root() was simplified in ape 3.4, so this needs to be
checked carefully. Can you send me this tree (privately)?
Cheers,
Emmanuel
Le 01/04/2016 18:49, Li, Fan a écrit :
Hi all,
I'm using the latest ape version (v3.4) under R 3.2.3 Patched. When I try to
root an unrooted 'phylo' object with the outgroup as either of the first two
tips in my tree, and with resolve.root=T, I get this error:
phy
Phylogenetic tree with 658 tips and 656 internal nodes.
Tip labels:
4373152, 975306, 708680, 508968, 199524, 176604, ...
Node labels:
, 0.941, 0.246, 0.913, 0.850, 0.759, ...
Unrooted; includes branch lengths.
failures <- {}
for (tip in phy$tip.label) {
+ outval <- try(root(phy, tip, resolve.root=T), silent=T)
+ if (class(outval) == "try-error") {
+ failures <- c(failures, tip)
+ }
+ }
failures
[1] "4373152" "975306"
which(phy$tip.label==failures)
[1] 1 2
Tracing the error to line 259 of root.R, which checks the 'fuseRoot' variable
but this has not been set if (newroot == ROOT) at line 155. I'm not familiar
enough with the code to know if fuseRoot should be FALSE or TRUE in this case,
but just wanted to point this out.
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