Ahhh, I thought since it says 'Empirical' I thought the CI estimate was for the observed Mantel r value, not for the permuted values. 

That makes sense now. 

Thanks, 

______________________Scott Chamberlain
Rice University, EEB Dept.


On Thursday, June 9, 2011 at 5:06 PM, Jari Oksanen wrote:

> On 10/06/11 00:12 AM, "Scott Chamberlain" <scttchamberlain4@gmail.com (mailto:scttchamberlain4@gmail.com)>
> wrote:
> 
> > How is it possible that the upper confidence limit of mantel's r is below that
> > of the estimate r value itself?
> > 
> > For example, using the example in the vegan documentation:
> > require(vegan)
> > data(varespec) data(varechem) veg.dist <- vegdist(varespec) # Bray-Curtis
> > env.dist <- vegdist(scale(varechem), "euclid") mantel(veg.dist, env.dist)
> > Mantel statistic based on Pearson's product-moment correlation Call:
> > mantel(xdis = veg.dist, ydis = env.dist) Mantel statistic r: 0.3047
> > Significance: 0.001 Empirical upper confidence limits of r: 90% 95% 97.5% 99%
> > 0.110 0.145 0.173 0.196 Based on 999 permutations
> > 
> > 
> > The 95% confidence limit is below that of the 0.3047 estimate. I must be
> > reading this wrong. Is the 95% limit supposed to be the amount +/- of the
> > estimate of r? 
> Perhaps your observed value is "significant" in which case it is outside 95%
> of the permuted values?
> 
> Cheers, Jari Oksanen


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