Thank you all very much for the comments! They are so helpful.
Yes, I do only have 8 species, and 3 replicates each. It is not ideal, but it's
what we have and we have a phylogeny, so I'd like to try some tests
incorporating phylogeny.
I probably should have added that I plan on running OLS to
From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Andrea
Berardi [andrea.bera...@colorado.edu]
Sent: Monday, March 02, 2015 3:57 PM
To: r-sig-phylo@r-project.org
Cc: Anthony R Ives; Peter Smits
Subject: Re: [R-sig-phylo] phytools - evaluating significance of pgls.Ives
, 2015 2:49 PM
To: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] phytools - evaluating significance of pgls.Ives
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On 15-03-01 11:40 PM, Simon Blomberg wrote:
Am I missing something? The OP only has 8 species in the data set.
I wouldn't put
R
Ives [ari...@wisc.edu]
Sent: Monday, March 02, 2015 2:14 PM
To: Andrea Berardi
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] phytools - evaluating significance of pgls.Ives
Andrea,
I second Liam’s recommendation to use a LRT.
For measurement error, the latest code I have in matlab
Blackwell
From: R-sig-phylo
[r-sig-phylo-boun...@r-project.org] on behalf of Anthony R Ives
[ari...@wisc.edu] Sent: Monday, March 02, 2015 2:14 PM To: Andrea
Berardi Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo]
phytools - evaluating
] on behalf of Ben Bolker
[bbol...@gmail.com]
Sent: Monday, March 02, 2015 2:49 PM
To: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] phytools - evaluating significance of pgls.Ives
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On 15-03-01 11:40 PM, Simon Blomberg wrote:
Am I missing something
Hi all,
I'm just learning how to do PGLS analyses, and I'm looking for advice on how to
evaluate the significance of the regression fit using pgls.Ives in the phytools
package. I'm using this function because it incorporates sampling error of
species means, and my data has about 3 individuals
Hi Andrea.
This is not presently implemented, but since this is a likelihood method
it would be straightforward to constrain to a slope of zero and then do
a LR test. This would be probably be the easiest way to test a
hypothesis about the regression.
That being said, as noted in the
Andrea,
I second Liam’s recommendation to use a LRT.
For measurement error, the latest code I have in matlab is MERegPHYSIGv2.m,
which does both measurement error and an OU or Pagel-lambda transform (see
Johnson, M. T. J., A. R. Ives, J. Ahern, and J. P. Salminen. 2014.
Macroevolution of
