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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_{A,B Chao1}}{S1_{chao} + S2_{chao} - S_{A,B Chao1}}</math>,   
+
<math>S_{Jest} = \frac{S_{A,B Chao}}{S1_{chao} + S2_{chao} - S_{A,B Chao}}</math>,   
  
  
 
where,
 
where,
  
<math>S_{A,B Chao1}</math> = estimated number of OTUs shared between A and B using the SharedChao1 estimator.
+
<math>S_{A,B Chao}</math> = estimated number of OTUs shared between A and B using the <math>S_{A,B Chao}</math> estimator.
S1chao = number of OTUs estimated in A using the Chao estimator.
+
S2chao = number of OTUs estimated in B using the Chao estimator.
+
  
 +
<math>S1_{chao}</math> = number of OTUs estimated in A using the Chao estimator.
  
For this example the value was 0.88.
+
<math>S2_{chao}</math> = number of OTUs estimated in B using the Chao estimator.
 +
 
 +
 
 +
At distance 0.03, the <math>S_{Jest}</math> value is 0.705297.

Revision as of 17:09, 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 Chao}}{S1_{chao} + S2_{chao} - S_{A,B Chao}}</math>,


where,

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

<math>S1_{chao}</math> = number of OTUs estimated in A using the Chao estimator.

<math>S2_{chao}</math> = number of OTUs estimated in B using the Chao estimator.


At distance 0.03, the <math>S_{Jest}</math> value is 0.705297.