# User guide

## Estimated true prevalence using one test with a Gibbs sampler

This analysis uses a Bayesian approach and Gibbs sampler to estimate the true animal-level prevalence of infection based on testing of individual (not pooled) samples using a test with imperfect sensitivity and/or specificity. The analysis requires prior estimates of true prevalence, test sensitivity and test specificity as Beta probability distributions, and outputs posterior distributions for prevalence, sensitivity and specificity. See Joseph et al. (1995) for more details.

Required inputs for this analysis are:

- assumed true prevalence,
- estimated test sensitivity and
- estimated test specificity.

The number of samples tested must be a positive integer and the number of positive samples must be an integer >=0 and <= the number of samples tested. Alpha and beta parameters for prevalence, sensitivity and specificity must be >0 and upper and lower confidence limits must be >0 and <1. Starting values for the numbers of true positives and false negatives must be integers >= zero and <= the number of positive samples and the number of negative samples, respectively. The number of iterations and the number discarded must both be positive integers (>0) and the number discarded must be less than the number of iterations.

The Gibbs sampler is used to estimate the posterior probability distributions of true prevalence, sensitivity and specificity that best fit the data and the prior distributions provided.

Prior estimates of the true prevalence and test sensitivity and specificity may be based on expert
knowledge or on previous data. These estimates are specified as
Beta probability distributions, with parameters alpha and
beta. Beta probability distributions are commonly used to express uncertainty about a proportion
based on a random sample of individuals. In this situation, if x individuals are positive for a
characteristic out of n examined, then the alpha and beta parameters can be calculated as alpha = x + 1
and beta = n - x + 1. Alternatively, alpha and beta can be calculated using the
*Beta distribution utility*, provided estimates of
the mode and 5% or 95% confidence limits are available from expert opinion.

Outputs from the Gibbs sampler are posterior probability distributions for:

- animal-level prevalence,
- test sensitivity,
- test specificity,
- positive and negative predictive values for the test,
- positive and negative likelihood ratios for the test and
- the numbers of true-positive and false-negative test results.

These distributions are described by their:

- minimum,
- lower probability limit,
- median,
- upper probability limit,
- maximum,
- mean and
- standard deviation.
- histogram and density chart (download by clicking on the appropriate icon).
- text files of parameter estimates for all iterations of the Gibbs sampler (download by clicking on the appropriate icon).

Because the Gibbs sampler estimates prevalence iteratively, based on the data and the prior distributions, it may take a number of iterations for the model to converge on the true value. Therefore, a specified number of initial iterations must be discarded (not used for estimation) to allow the model to converge on the true values. This number must be sufficient to allow convergence, and should be at least 2000 - 5000. It is also important to carry out an adequate number of iterations to support inference from the results. Suggested minimum values for the total number of iterations and the number to be discarded are provided, but can be varied if desired.

This analysis may take several minutes to complete, depending on the number of iterations required.