[Mesquitelist] PDAP and ICs

[Wayne Maddison]

The two ways to get values across a sample of trees is through
-- a chart for the trees
-- a script you write to scroll through the trees in the tree window, 
and output results to a text file for each tree.

For your needs you 'd have to do the script, and ask the PDAP chart 
to save its text to a file.  The problem with this is that the output 
won't be convenient for you, as it is not in a simple parsable format.

We are working to make it easier to get such results.  What would be 
your ideal output?  A tab delimited table, one row per tree, with
treenameOrNumber1 <tab> contrast at first node <tab> contrast at 
second node ...
treenameOrNumber2 <tab> contrast at first node <tab> contrast at 
second node ...

?

Would you want two characters in the same file, or as two separate 
files?  Would it bo OK if the sequence of nodes in subsequent trees 
to be not guaranteed to be comparable?  (i.e. the Rosaceae might be 
represented as the 10th node in the first tree, but the 30th node in 
the next tree)

Wayne


At 5:05 PM -0700 18.4.2008, dhearn at email.arizona.edu wrote:
>Hi all,
>
>I am interested in calculating contrast values across a sample of 
>trees from the
>posterior distribution of a Bayesian analysis. The comparisons include
>continuous X continuous and binary X continuous variables. I have a couple
>questions...
>
>Is there a way to adapt PDAP, or ar there features in place, to print out
>contrast values across a sample of trees?
>
>Are there any features similar to CAIC's crunch and brunch options that permit
>the comparison of one dichotomous trait and one continuous trait?
>
>Many thanks,
>David
>
>
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-- 
--------------------------------------------------------
Wayne Maddison
  Professor and Canada Research Chair
          Depts. of Zoology and Botany and
          Biodiversity Research Centre
  & Director
          Beaty Biodiversity Museum
  6270 University Boulevard
  University of British Columbia
  Vancouver, BC  V6T 1Z4   Canada

email: wmaddisn at interchange.ubc.ca   FAX: (604) 822-2416

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