Hello, the original question was https://www.mail-archive.com/r-sig-phylo@r-project.org/msg05367.html Playing with the 'power' parameter of the compute.brlen() function was the only I found working. Thank You both, V.
Dne středa 12. prosince 2018 20:31:11 CET jste napsal(a): > I didn't see the email that this addresses, but I will add a couple of > comments to Juan's suggestion: > (1) phytools::cophylo does not require the input trees to have branch > lengths. If they do not, arbitrary branch lengths for plotting are > computed using ape::compute.brlen. > (2) The code suggested by Juan does indeed assign branch lengths to the > tree; however, it has effect of assigning different depths for > equivalently nested relationships. If you don't like the spacing of > compute.brlen, it is possible to change it using the argument 'power.' > 0<power<1 results in divergences between sister taxa pushed backward in > time & may look better than the default. > All the best, Liam > > On 12/12/2018 12:07 PM, Juan Antonio Balbuena wrote: > > You can try this: > > tree<- compute.brtime(tree, tree$Nnode:1) > > It will produce an ultrametric tree with its nodes well separated. > > I hope it helps > > All the best -- Vojtěch Zeisek https://trapa.cz/en/ Department of Botany, Faculty of Science Charles University, Prague, Czech Republic https://www.natur.cuni.cz/biology/botany/ Institute of Botany, Czech Academy of Sciences Průhonice, Czech Republic http://www.ibot.cas.cz/en/
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