bootstrapping

[sylvia hope]

As James Whitfield indicated, the bootstrap has indeed been variously
interpreted.  From my perspective, perhaps the most important assumption
of the boostrap as uysually applied in phylogenetics is the assumption of
external validity;, i.e., the variability found in the total of N
pseudoreplicate resampling of the matrix is supposed to reflect the type
of variability that would be found if N additional true samples were
taken.  The boostrap cannot be used to test this assumption, obviously,
and therefore the distinction between precision and accuracy is clear.

          The problem in my mind is that people who use the boostrap
          [sic] don't usually note in their presentation that it does
          not indicate external validity.

          A high bootstrap value for a particular clade can be due to
          biased sampling of characters that are functionally related,
          maybe by a focus on a limited anatomical complex, or a
          single gene.

          Even if characters are many and varied in the matrix the
          bootstrap can be misleading.  Again I belabor the // with
          psych tests - usually they have a panorama of questions that
          *seem* on the face of it to be relevant to some
          characteristic they want to assess - and there may be high
          reliability but low validity by some outside criterion (for
          example, a personality test with pscyhiatric diagnosis or
          school grades with IQ test).

          This is the reason that I don't like the idea of combining
          disparate data into a single set - if you keep different
          kinds of data separate each data matrix provides an external
          criterion of validity .



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Sylvia Hope
Dept. of Ornithology and Mammalogy    *
California Academy of Sciences        *
Golden Gate Park                      *
San Francisco, CA, USA 94118          *
                                      *
email:  sylvia.hope at calacademy.org    *
phone:  (415) 750-7176                *
fax:    (415) 750-7137                *
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