I am currently using the geiger package to do this calculation (function fitContinuous() ) but it does not have an option to do a likelihood ratio test (LRT) to evaluate the significance of lambda. It does give you the loglikehood values from the Maximum likelihood estimation, so it is possible to do the LRT but one needs to do it manually. If someone knows if it is possible to automate this procedure it would save me a lot of time.
Hi,
Try Liam Revell's package "phytools". Particularly function "phylosig" can be useful for you. I have never tried it, but I remember that I have read about that possibility.
Here are some useful links:
http://cran.r-project.org/web/packages/phytools/phytools.pdf
http://blog.phytools.org/2012/01/fitting-pagels-for-single-trait-using.html
http://blog.phytools.org/2012/11/testing-for-pagels-10.html
http://evolbiology.blogspot.com/2012/10/when-to-use-phylogenetic-comparative.html
Hope this helps.
Here is a link that might help: http://www.anthrotree.info/wiki/pages/n4j2K1j0/531_Estimating__in_R_geiger_caper.html
Hi,
Try Liam Revell's package "phytools". Particularly function "phylosig" can be useful for you. I have never tried it, but I remember that I have read about that possibility.
Here are some useful links:
http://cran.r-project.org/web/packages/phytools/phytools.pdf
http://blog.phytools.org/2012/01/fitting-pagels-for-single-trait-using.html
http://blog.phytools.org/2012/11/testing-for-pagels-10.html
http://evolbiology.blogspot.com/2012/10/when-to-use-phylogenetic-comparative.html
Hope this helps.
If you are doing Phylogenetic Generalized Least Squares, then the pgls() function in the caper package automatically provide likelihood ratio test results for lambda.
I found this post about the limitations of lambda. You might take a look.
http://carlboettiger.info/2013/10/11/is-it-time-to-retire-pagels-lambda.html
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