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
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--
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:
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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
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