Hello, Liam, no, it's not complicated. I was just wondering if anyone has some more elegant solution or if I don't do anything wrong. Thank You, Vojtěch
Dne čtvrtek 13. prosince 2018 14:24:09 CET jste napsal(a): > Hello Vojtěch. > To me, it doesn't seem much more difficult for the user to specify: > object <- cophylo(compute.brlen(phy1,power=0.5), > compute.brlen(phy2,power=0.7)) ## or what have you > than: > object <- cophylo(phy1,phy2,power=c(0.5, 0.7)) > and then have power passed internally to compute.brlen. Is that > what you'd prefer? > All the best, Liam > > On 12/12/2018 6:29 PM, Vojtěch Zeisek wrote: > > 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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