Dear members:
Does anyone know of scripts to both estimate and test
phylogenetically-corrected RMA regression slopes (perhaps using the relevant
equations from Ives et al. (Syst. Biol. 2007))?
Cheers,
Arne Mooers
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Dr. Arne Mooers
Biological Sciences,
Simon
Hi Arne,
Just calculating the slope is straightforward. For tree and column
vectors x y (in order tree$tip.label):
C-vcv.phylo(tree)
ax-sum(solve(C,x))/sum(solve(C))
ay-sum(solve(C,y))/sum(solve(C))
beta1-sqrt(t(y-ay)%*%solve(C,y-ay)/(t(x-ax)%*%solve(C,x-ax)))
The model intercept can
Dear R users,
I am trying to compare correlation's among traits without phylogeny and with
accounting for phylogenetic history (each data point is a species mean trait
value). There is no clear predictor and no clear response variable between two
traits.
I thought that regression through
Liam said:
Just calculating the slope is straightforward. For tree and column
vectors x y (in order tree$tip.label):
The relevant point to keep in mind is that once you
have made maximum likelihood estimates of the means,
variances and covariances of the variables, the
Reduced Major Axis
Scott,
I would love it if somebody would. If I were doing it now, I'd
simultaneously use an OU or maybe lambda transform. Several people
have code that does, for example, regression while assuming residual
variation has some non-Brownian phylogenetic structure (e.g., Lavins
et al.
I think it is important to point out, that while RMA may superficially
be an attractive method, it relies on the ratio of error variances
being unity. This is almost always incorrect. It usually results in a
massive over-correction of the slope bias with respect to the OLS
estimator. That is,
