Bootstrap and Happiness

newsmgr at merrimack.edu newsmgr at merrimack.edu
Fri Dec 19 17:41:06 EST 1997

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Subject: Bootstrap and  Happiness 
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On a website <<http://cmgm.Stanford.EDU/phylip/seqboot.html>> I found the
following statement:

<<The R option allows the user to set the number of replicate data sets. This
defaults to 100. Most statisticians would be happiest with 1000 to 10,000
replicates in a bootstrap, but 100 gives a good rough picture. You will have to
decide this based on how long a running time you want.>>

My question is how happiness of a statistician is related to statistical
significance. Using GCG-PAUP I found that with neighbor-joint option I will get
very different results using 100, 1,000 or 10,000 replicates in one particular
case. The same is true for the parsimony option. However, results obtained with
10,000 replicates with N-J option are similar to results obtained with 1,000
replicates with P option.It seems like to achieve the same state of happiness
it requires only 1,000 P versus 10,000 N J.  I would greatly appreciate any
comments on this issue.

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