Re: [R-sig-phylo] multi2di fails on multiPhylo objects

Hi, Klaus: thanks for the fix. There is a development version on ape-package.ird.fr: http://ape-package.ird.fr/ape_installation.html#versions This version is 4.0-0.2. The source as well as a Windows version are avaialble. The list of changes is there: http://ape-package.ird.fr/NEWS Best,

Re: [R-sig-phylo] multi2di fails on multiPhylo objects

On 13 Jan 2017, at 20:37, Klaus Schliep wrote: > Hi Yan, > > it seems we introduced a small bug with making these functions generic. > Replace in the function .multi2di_ape the line > phy <- reorder(phy) > with > phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L)

Re: [R-sig-phylo] multi2di fails on multiPhylo objects

On 13 Jan 2017, at 20:37, Klaus Schliep wrote: > Hi Yan, > > it seems we introduced a small bug with making these functions generic. > Replace in the function .multi2di_ape the line > phy <- reorder(phy) > with > phy <- .reorder_ape(phy, "cladewise", FALSE, n,

Re: [R-sig-phylo] multi2di fails on multiPhylo objects

Hi Yan, it seems we introduced a small bug with making these functions generic. Replace in the function .multi2di_ape the line phy <- reorder(phy) with phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L) and it should work. You have to recompile ape afterwards. Cheers, Klaus On Fri, Jan 13,

Re: [R-sig-phylo] multi2di fails on multiPhylo objects

Thanks. I think that’s because read_nexus_phylo() doesn’t do .compressTipLabel automatically n <- read_nexus_phylo("tmp.nex") n2 <- .compressTipLabel(n) multi2di(n2) #this causes an error. Unfortunately I need the .compressTipLabel functionality really. Yan On 13 Jan 2017, at 17:06, François

[R-sig-phylo] multi2di fails on multiPhylo objects

If I have a nexus file with multiple trees, and the same tips in each tree, but some trees with polytomies, like this #NEXUS BEGIN TREES; TRANSLATE 1 1, 2 2, 3 3, 4 4; TREE A = (((1,2)5,3)6,4); TREE B = ((1,2,3)6,4); END; Then when I try to resolve both trees using multi2di, I get > n <-