Calculate least-cost sample sizes for 2-stage surveys for demonstrating disease freedom,
where herd sizes are unknown.
This analysis calculates the number of herds and the number of animals within each herd
to be tested to provide a specified system sensitivity (probability of detecting disease)
for the given animal and herd-level design prevalences and test sensitivity,
where actual herd sizes are unknown. Test
specificity is assumed to be 100% (or follow-up testing of any positive will be undertaken
to confirm or exclude disease).
Sample sizes are optimised to minimise overall cost for given herd and animal-level
testing costs. A maximum sample size per herd must be specified and either
the number of herds in the population or a maximum number of herd to be tested
must be specified.
Numbers of animals to test in each herd are calculated using assumed binomial sampling
(sample size is small relative to herd sizes), while numbers of herds to test are
calculated using the HerdPlus algorithm, based on the hypergeometric
probability distribution (sampling without replacement) if the number of herds in the
population is specified or assuming binomial sampling if not.
Design prevalence (specified level of disease to be detected) must be specified
at both animal and herd levels. Design prevalence can be specified as either:
- a proportion of the population infected; or
- a specific (integer) number of herds infected (for herd-prevalence only and
only if the number of herds in the population is specified).
Inputs required include:
- animal-level design prevalence (as a proportion only);
- herd-level design prevalence and whether this is specified as a proportion or number of herds;
- the estimated test sensitivity;
- the relative cost of testing at both herd and animal levels;
- the target system sensitivity (SSe) which is the probability of detecting
disease if it is present at the specified design prevalences;
- the maximum sample size to be tested per herd; and
- The number of herds in the population OR the maximum number of herds
to be tested.
Outputs from the analysis include:
- A summary of the total numbers of herds and animals to be sampled,
target number of animals to test per herd, estimated SeH per herd and the achieved SSe;
- A summary of numbers of herds to be tested and corresponding numbers of
animals to test in each herd, the estimated SeH and the relative cost for each option; and
- An excel spreadsheet and graph of the summary results.
If it is not possible to achieve the desired system sensitivity by testing the
specified maximum number of animals in all (or the specified maximum number) of the
herds, a message will be
returned, along with a summary of the achieved mean SeH and SSe if the maximum numbers
of animals and herds were