I beg his pardon. This is David Orme, of course, not David Ackerley On Mon, Feb 1, 2016 at 12:54 PM, James Rodger <rodge...@gmail.com> wrote:
> Dear Rizwana and Simon, > > see also this reply from David Ackerley to a question of mine on r-squared > in pGLS > > http://www.mail-archive.com/r-sig-phylo%40r-project.org/msg03953.html > > regards, > > James > >> >> >> Date: Fri, 29 Jan 2016 10:06:05 +1000 >> From: Simon Blomberg <s.blombe...@uq.edu.au> >> To: r-sig-phylo@r-project.org >> Subject: Re: [R-sig-phylo] interpreting pGLS >> Message-ID: <56aaaced.3020...@uq.edu.au> >> Content-Type: text/plain; charset=windows-1252; format=flowed >> >> Hi Rizwana, >> >> There is no reason why we would expect the phylogenetic signal in the >> raw variables to be the same as the phylogenetic signal from the >> regression analysis (K or lambda), as in the regression, you are really >> looking at the phylogenetic signal of the _residuals_, which may be >> quite different. Also, the r-squareds from pgls in caper are not >> calculated in the same way as r-squareds from an ordinary least squares >> analysis. In fact, there is no "correct" way to calculate r-squared for >> any model other than the OLS model, as OLS r-squared is based on the >> residual variance. For other types of models, including GLS, "residual >> variance" is not a well-defined concept. Personally, I don't use >> r-squared for any model other than OLS models. There are far better ways >> to conduct model criticism. >> >> Cheers, >> >> Simon. >> >> On 28/01/16 15:57, Rizwana Rumman wrote: >> > Dear R-sid-phylo list, >> > >> > I am having some problems to interpret the results of a co-evolution >> analysis and I hope you can help me to get my head around things. >> > >> > I have two variables that each show significant non-random phylogenetic >> signal (K and lambda) and appear to be significantly correlated in a >> non-phylogenetic regression; but when I am performing a pGLS in caper, the >> lambda is estimated to be zero and the two variables shows the exact same >> R-square and level of significance as estimated from the non-phylogenetic >> regression analysis. I also have two other sets of variables that show >> lambdas >0 (very similar values from caper and ape) in the pGLS analysis, >> but for these variables, the R-square values are smaller from pGLS than >> those estimated from non-phylogenetic regression. I guess my question is if >> I can safely interpret that, in the first case, phylogenetic history does >> not significantly affect my trait correlations (indicated by lambda=0 and >> very similar simple linear regression and pGLS results) and in the latter >> case (i.e. smaller R-squares after correcting for phylogeny), >> non-phylogenetic regressions slightly overes! >> ti! >> > mates the correlations of the traits. >> > >> > Many thanks for the help! >> > >> > Cheers, >> > Rizwana >> > >> > >> > [[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/ >> >> -- >> Simon Blomberg, BSc (Hons), PhD, MAppStat, AStat. >> Senior Lecturer and Consultant Statistician >> School of Biological Sciences >> The University of Queensland >> St. Lucia Queensland 4072 >> Australia >> T: +61 7 3365 2506 >> email: S.Blomberg1_at_uq.edu.au >> http://www.evolutionarystatistics.org >> >> Policies: >> 1. I will NOT analyse your data for you. >> 2. Your deadline is your problem. >> >> Basically, I'm not interested in doing research >> and I never have been. I'm interested in >> understanding, which is quite a different thing. >> - David Blackwell >> >> >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> >> ------------------------------ >> >> End of R-sig-phylo Digest, Vol 96, Issue 17 >> ******************************************* >> > > [[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/
