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Difference between revisions of "Jest"

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Estimating the fraction of sequences that belong to shared OTUs.
 
Estimating the fraction of sequences that belong to shared OTUs.
  
Just as the Chao1 richness estimator is a function of the number of OTUs observed once or twice in a sample (6), the estimators of the fraction of sequences in shared OTUs is a function of the number of shared OTUs that are observed at least once or twice in the community being analyzed (8, 7). <math> S_{Jest}</math> is essentially a form of the equation for <math>J_{abund} </math> that is not corrected for the presence of unsampled OTUs.
+
Just as the Chao1 richness estimator is a function of the number of OTUs observed once or twice in a sample (6), the estimators of the fraction of sequences in shared OTUs is a function of the number of shared OTUs that are observed at least once or twice in the community being analyzed (8, 7). <math> S_{Jest}</math> is essentially a form of the equation for <math>{J_{abund}} </math> that is not corrected for the presence of unsampled OTUs.
  
  
  
<math>S_{Jest} = \frac{S_{sharedChao1}}{S1_{chao} + S2_{chao} - S_{sharedChao1}}</math>,   
+
<math>S_{Jest} = \frac{S_{A,B Chao1}}{S1_{chao} + S2_{chao} - S_{A,B Chao1}}</math>,   
  
  
 
where,
 
where,
  
Ssharedchao1 = estimated number of OTUs shared between A and B using the SharedChao1 estimator.
+
<math>S_{A,B Chao1}</math> = estimated number of OTUs shared between A and B using the SharedChao1 estimator.
 
S1chao = number of OTUs estimated in A using the Chao estimator.
 
S1chao = number of OTUs estimated in A using the Chao estimator.
 
S2chao = number of OTUs estimated in B using the Chao estimator.
 
S2chao = number of OTUs estimated in B using the Chao estimator.

Revision as of 17:06, 15 January 2009

Validate output by making calculations by hand


Example Calculations

*.sharedJest

Estimating the fraction of sequences that belong to shared OTUs.

Just as the Chao1 richness estimator is a function of the number of OTUs observed once or twice in a sample (6), the estimators of the fraction of sequences in shared OTUs is a function of the number of shared OTUs that are observed at least once or twice in the community being analyzed (8, 7). <math> S_{Jest}</math> is essentially a form of the equation for <math>{J_{abund}} </math> that is not corrected for the presence of unsampled OTUs.


<math>S_{Jest} = \frac{S_{A,B Chao1}}{S1_{chao} + S2_{chao} - S_{A,B Chao1}}</math>,


where,

<math>S_{A,B Chao1}</math> = estimated number of OTUs shared between A and B using the SharedChao1 estimator. S1chao = number of OTUs estimated in A using the Chao estimator. S2chao = number of OTUs estimated in B using the Chao estimator.


For this example the value was 0.88.