Re: [R-sig-phylo] Plotting character data next to tree in R

Hi Katharine. You can try to search my blog for examples of the function add.simmap.legend. That might do what you want. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu

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

Re: [R-sig-phylo] Amniote Phylogenetic Tree

Hi Sergio, You might find what you want within the Open Tree of Life (http://tree.opentreeoflife.org/) whose content can be accessed from R with the rotl package (https://cran.r-project.org/web/packages/rotl/index.html) Cheers, -- François On Fri, Jan 13, 2017 at 7:04 AM, Sergio Ferreira

[R-sig-phylo] Amniote Phylogenetic Tree

Hello all, Do you know of any database where one can obtain a good phylogeny of the Amniota (in NEXUS or NEWICK file)? Thank you. Best regards, Sérgio. -- Com os melhores cumprimentos, Sérgio Ferreira Cardoso. Best regards, Sérgio Ferreira Cardoso MSc. Paleontology

[R-sig-phylo] Plotting character data next to tree in R

Hi, I am trying to visualize a few different character traits on a tree using phytools. My tiplabels are colored by sampling location and I'd like to add alongside the tree a color bar that represents values of a discrete character trait (bacterial serotypes) for each tip sample. There is a nice

[R-sig-phylo] Introduction to R and statistics for biologists - CHINA - April2017

"Introduction to R and statistics for biologists" Delivered by Dr. Luc Bussiere and Dr. Ane Timenes Laugen http://www.prstatistics.com/course/introduction-to-statistics-and-r-for-biologists-irfb02/ This course will run from 17th – 21st April 2017 at FAFU University, Fuzhou, China A more

[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 <-