1-Stage Freedom analysis
# Calculate cluster-level sensitivity and specificity for range of sample sizes and cut-points for given cluster size and imperfect tests

### Inputs include:

### Outputs include:

This utility calculates cluster sensitivity (SeH) and cluster specificity (SpH) for a range of sample sizes and cut-point numbers of reactors, for specified cluster size, test sensitivity, test specificity and design prevalence values. Options for calculations include four different estimation methods:

- Binomial distribution: where cluster size is not specified;
- HerdPlus: Using the hypergeometric distribution;
- HerdAcc: Jordan D, McEwen SA, 1998. Herd-level test performance based on uncertain estimates of individual test performance, individual true prevalence and herd true prevalence.
*Prev. Vet. Med.***3**: 187-209; and - FreeCalc: Cameron AR, Baldock FC, 1998. A new probability formula for surveys to substantiate freedom from disease.
*Prev. Vet. Med.***34**: 1-17.

- Test sensitivity and specificity;
- Specified cluster/population size;
- Maximum and minimum sample sizes to be considered and the step in values;
- Up to 5 unit-level design prevalences (the hypothetical prevalence to be detected, as proportions);
- Maximum and minimum cut-point number of positives to classify a cluster (herd/flock) as positive;
- The preferred calculation method; and
- The desired precision of results (number of digits to be displayed after the decimal point).

- Tables and plots of SeH and SpH for each design prevalence value for combinations of sample size and cut-points; and
- An excel file of the results.