[Mesquitelist] Presentation of multiple likelihood-ratio tests, extraction of multiple P values from Mesquite

[Nina Hobbhahn]

Dear fellow list users,

I apologize for re-posting this, but there were no replies to my previous postings. Any input would be greatly appreciated.

Thank you for your time,

Nina

Begin forwarded message:

> From: Nina Hobbhahn <n.hobbhahn at gmail.com>
> Subject: Presentation of multiple likelihood-ratio tests, extraction of multiple P values from Mesquite
> Date: 28 March, 2012 1:36:21 PM GMT+02:00
> To: mesquitelist at mesquiteproject.org
> 
> Dear fellow list users,
> 
> I am using the following likelihood-ratio tests in Mesquite to examine the evolution of a binary trait over a phylogeny:
> 
> 1. Asymmetry likelihood-ratio test to compare asymmetrical and one-parameter models of trait evolution
> 2. BiSSE ln likelihood difference for a) speciation rate, b) extinction rate, and c) diversification rate.
> 
> I am running these analyses over a sample of 1000 trees to account for phylogenetic uncertainty. To do this, I open a New Bar & Line Chart for Trees under "Analysis" and set up the analyses. The output then contains mean, median, and 95% confidence intervals for the likelihood-ratio statistic D. 
> 
> My questions are:
> 
> 1. Is it statistically correct to present average D values with their 95% confidence intervals? If not, could you please advise how the results from multiple LH-ratio tests should be presented?
> 
> 2. IF I present average D values, is it correct to use the chi-square value with the corresponding number of degrees of freedom for assessment of statistical significance?
> 
> 3. Alternatively, one could follow the approach by DeWitt Smith et al (2008, in Evolution 62(4): THE ROLE OF POLLINATOR SHIFTS IN THE FLORAL DIVERSIFICATION OF IOCHROMA (SOLANACEAE)), who report the average P value from multiple comparisons. IF this approach is preferable to that suggested in 2., then
> 
> 4. How can I extract not only the LH-ratio values for each tree, but also the associated P values from Mesquite?
> 
> 
> Thank you very much for your interest and time,
> 
> Nina
> 
> 
> 
> Dr. Nina Hobbhahn
> Post-doctoral fellow
> Lab of Prof. S. D. Johnson
> School of Life Sciences
> University of KwaZulu-Natal
> Private Bag X01
> Scottsville, Pietermaritzburg, 3201
> South Africa
> 



Dr. Nina Hobbhahn
Post-doctoral fellow
Lab of Prof. S. D. Johnson
School of Life Sciences
University of KwaZulu-Natal
Private Bag X01
Scottsville, Pietermaritzburg, 3201
South Africa

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