# Difference between revisions of "Jest"

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). ${S_{Jest}}$ is essentially a form of the equation for $J_{abund}$ that is not corrected for the presence of unsampled OTUs.

$S_{Jest} = \frac{S_{A,B Chao}}{S1_{chao} + S2_{chao} - S_{A,B Chao}}$,

where,

$S_{A,B Chao}$ = estimated number of OTUs shared between A and B using the $S_{A,B Chao}$ estimator.

$S1_{chao}$ = number of OTUs estimated in A using the Chao estimator.

$S2_{chao}$ = number of OTUs estimated in B using the Chao estimator.

At distance 0.03, the ${S_{Jest}}$ value is 0.705297.

References

6. Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11:265-270.

7. Chao, A., R. L. Chazdon, R. K. Colwell, and T. J. Shen. 2006. Abundance-based similarity indices when there estimation when there are unseen species in samples. Biometrics 62:361-371.

8. Chao, A., R. L. Chazdon, R. K. Colwell, and T. J. Shen. 2005. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol. Lett. 8:148-159.