Dear Emmanuel and Alejandro Many thanks for your replies.
Emmanuel, I understand what you said if I use vcv(nonultrametric_tree, cor=FALSE) in a phylogenetic comparative method (PCM). But if I use vcv(nonultrametric_tree, cor=TRUE), isn't this the same as assuming a ultrametric tree? I may be missing something here? Note that vcv(nonultrametric_tree, cor=TRUE) is different from vcv(chronoMPL(nonultrametric_tree), cor = TRUE), which is relates to my previous question (which one is preferred?) Many thanks Shinichi On Sun, Oct 30, 2016 at 9:53 AM, Alejandro Gonzlaez Voyer < alejandro.gonza...@iecologia.unam.mx> wrote: > Hi, > > I would venture in adding that with an additive tree the differences in > evol rates among species are determined by the genes used to estimate the > tree, given differences in substitution rates among genes. I do think its > important to bear in mind. > > Cheers > > Alejandro > > Alejandro Gonzalez Voyer > Instituto de Ecologia > UNAM > > > > > > On Oct 29, 2016, at 2:45 PM, Emmanuel Paradis <emmanuel.para...@ird.fr> > wrote: > > > > Sure they are different. I forgot to mention that. > > > > In comparative analyses, the expected quantity of trait change (= the > variance in the VCV matrix) is given by the product of the rate of > evolution of the trait with branch length. So using a non-ultrametric tree > is a way to assume different rates of evolution for each branch. With an > ultrametric tree, you somehow assume a "clock-like" trait evolution (i.e., > the quantity of change from the root of the tree to the tips is the same). > > > > BTW, the first command you give below should be (misplaced right > parenthesis): > > > > vcv(chronoMPL(nonultrametric_tree), cor = TRUE) > > > > Best, > > > > Emmanuel > > > >> Le 29/10/2016 à 13:12, Shinichi Nakagawa a écrit : > >> Dear Emmanuel > >> > >> Many thanks for your swift reply. > >> > >> If we get a correlation matrix, via chronoMPL [i.e. > >> vcv(chronoMPL(nonultrametric_tree,cor=T))], this correlation matrix is > >> different from a correlation matrix obtained directly from vcv [i.e. > >> vcv(nonultrametric_tree, cor=T)]. > >> > >> Could you enlighten me about differences and why chronoMPL method might > >> be preferred? > >> > >> Best wishes and thanks in advance. > >> > >> Shinichi > >> > >> On Sat, Oct 29, 2016 at 8:50 PM, Emmanuel Paradis > >> <emmanuel.para...@ird.fr <mailto:emmanuel.para...@ird.fr>> wrote: > >> > >> Dear Shinichi, > >> > >> A fast solution is provided by the function chronoMPL in ape; it does > >> not require calibration points (see the references in the help page > of > >> this function for the assumptions). The function chronos (also in > ape) > >> is another possibility but it needs at least one calibration point > >> (though this can be fixed to unity at the root). > >> > >> Note that a correlation matrix can be calculated from a > non-ultrametric > >> tree: see the function vcv. > >> > >> Best, > >> > >> Emmanuel > >> > >> Le 29/10/2016 à 05:26, Shinichi Nakagawa a écrit : > >> > Dear List > >> > > >> > We would like make several non-ultrametic trees (based on > >> molecular data; > >> > downloaded from treeBASE) into ultrametric trees using R. Could > >> you advice > >> > us what is the best and the most general way of doing this please? > >> > > >> > We would like to use resultant ultrametric trees in phyologenetic > >> > comparative analysis (by turning into correlation matrices). > >> > > >> > Best wishes, > >> > > >> > Shinichi Nakagawa > >> > > >> > [[alternative HTML version deleted]] > >> > > >> > _______________________________________________ > >> > R-sig-phylo mailing list - R-sig-phylo@r-project.org > >> <mailto:R-sig-phylo@r-project.org> > >> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > >> > Searchable archive at > >> http://www.mail-archive.com/r-sig-phylo@r-project.org/ > >> <http://www.mail-archive.com/r-sig-phylo@r-project.org/> > >> > > >> > > >> > Pour nous remonter une erreur de filtrage, veuillez vous rendre > >> ici : http://f.security-mail.net/301dITcFgNy > >> <http://f.security-mail.net/301dITcFgNy> > >> > > >> > > >> > >> > >> > >> > > > > _______________________________________________ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
