[Biojava-dev] Distributions

[Schreiber, Mark]

Hi -

I have pulled out my copy of the Shannon paper and I'm 99% sure that the
shannon entropy calculation should be what is was before. Can someone
change it back or convince me I'm wrong.

- Mark

> -----Original Message-----
> From: Lachlan Coin [mailto:lc1 at sanger.ac.uk] 
> Sent: Thursday, 20 February 2003 10:31 p.m.
> To: jhidalgo at elmonte.es
> Cc: biojava-dev at biojava.org
> Subject: Re: [Biojava-dev] Distributions
> 
> 
> If you have a CVS checkout, you will find the code in
> 
> /biojava-live/src/org/biojava/bio/dist/DistributionTools.java
> 
> so, to calculate shannon entropy for a Distribution observed 
> to base 2, you can put
> 
> Map entropy = 
> DistributionTools.shannonEntropy(observedDistribution, 2)
> 
> which gives you a map of the information content of each 
> symbol in the alphabet (i.e. log(1/p(i))
> 
> You can also do:
> 
> double bits = 
> DistributionTools.bitsOfInformation(observedDistribution)
> 
> to get the total information context (which is just the 
> expectation of the above map under the observed distribution: 
> sum_i p(i)*log(1/p(i))
> 
> 
> Lachlan
> 
> 
> 
> 
> 
> 
> 
> On Thu, 20 Feb 2003 jhidalgo at elmonte.es wrote:
> 
> > Can anyone send me an example of ShannonEntropy calculation code?
> >
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at biojava.org 
> > http://biojava.org/mailman/listinfo/biojava-dev
> >
> 
> -------------------------------------------------------------
> Lachlan Coin
> Wellcome Trust Sanger Institute		Magdalene College
> Cambridge  CB10 1SA			Cambridge CB30AG
> Ph: +44 1223 494 820
> Fax: +44 1223 494 919
> ------------------------------------------------------------
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at biojava.org 
> http://biojava.org/mailman/listinfo/biojava-dev
> 
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