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Alfredo Tello (http://alfredotello.com)
Sustainable Aquaculture Group
Institute of Aquaculture
University of Stirling
Scotland, UK
Hi Folks,
Does anyone know if the p - values returned by the /ecodist/ mgram function
(mantel correlograms) are corrected for multiple testing? I'm aware
mantel.correlog in /vegan /has several correction options. I have gone
through the /ecodist/ paper, but still can't find an answer.
Thanks!
A
Hi Sarah,
Thanks for your reply. I've solved the problem (or at least gotten around
it). Dy is a Bray-Curtis dissimilarity matrix and Dx a euclidean matrix
representing an environmental gradient. I was running MRM as:
MRM(Dy~exp(Dx)). If I run MRM(log(Dy)~Dx) I don't get the error message.
Should
Sarah,
I don't think I've got the programming skills at the moment to contribute a
patch, but I'll keep it mind for the future. Thanks for the log()
reminder. It could definitely be tragic to confuse bases.
Best wishes,
A
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Hi Everyone,
MRM is returning what seems to be a matrix singularity error:
Error in solve.default(XX) :
system is computationally singular: reciprocal condition number =
1.88323e-86
when running MRM(Dy~exp(Dx)).
I would appreciate it if anyone could help me around this.
Thanks,
A
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Hi Jari,
Thanks for your prompt reply. That clears things up, although you've left me
with a doubt. You said:
Indeed, adonis() can use only continuous variables, it is documented to do
so, and this was initially intended.
Are you saying that categorical variables should not be used in
Thanks Jari! Sorry if I wasn't clear enough at first.
All the best,
A
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Sent from the r-sig-ecology mailing list archive at Nabble.com.
Hi Jari (and everyone else who might read this),
Just one last thing (I hope I'm not being annoying! ). I believe this can be
of interest to other people as well.
In a recent paper in the ISME (International Society for Microbial Ecology)
Journal, Thomas Bell used adonis to test for evidence of
Hi Folks,
The adonis documentation in vegan says that adonis accepts categorical
factors and/or continuous variables. I was aware (have seen it posted
somewhere else) that adonis could be run using a continuous variable as a
co-variate, but not that it could (or was initially intended to) be used
