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Validate output by making calculations by hand

Example Calculations


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_{sharedChao1}}{S1_{chao} + S2_{chao} - S_{sharedChao1}}</math>,


Ssharedchao1 = 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.