Bayesian taxon base rate

Next, Bayesian probabilities were computed and these produced a clear U-shaped pattern. The authors assigned cases with the probability of. 90 or above to the taxon, and found that 35 individuals were identified as taxon members by these rules, that is, the prevalence of this taxon was 3.3%. Note that the. 50 cutoff is generally associated with the lowest overall rate of misclassification, but the. 90 cutoff may be preferable under certain conditions. In epidemiological studies, however, accuracy—a low rate of misclassification—is the primary consideration. In fact, the actual prevalence of the taxon in the Waller and Ross study appears to be about 5% based on the non-Bayesian base rate estimates. Thus, it appears that the use of a conservative cutoff in this study may produce somewhat misleading findings. 

It is important to note that the base rate estimates were very close to. 50, suggesting that the results could have simply reflected sample selection. One way to rule out this type of possibility is to compute Bayesian probabilities and show that not all taxon members come from the clinical group. Bayesian probabilities cannot be computed with SSMAXCOV, but MAXCOV can do it. The empirical indicators were probably too short for MAXCOV, but it may have worked with the theoretical indicators, as they are much longer. Unfortunately this analysis was not performed. 

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