bootstrapping

[James Francis Lyons-Weiler]

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.

Other uses of the bootstrap can be used that don't require the same
assumption - for instance, any inference about the structure of the
matrix can be approached using any number of tests - as long as one
restricts the inferences to the characteristics of the matrix, internal
valdiity = external validity.  Conclusions about the _causes_ of
structure are a different matter.

James

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