epi.pooled {epiR} R Documentation

## Estimate herd test characteristics when pooled sampling is used

### Description

We may wish to designate a group of individuals (e.g. a herd) as being either diseased or non-diseased on the basis of pooled samples. This function estimates sensitivity and specificity of this testing regime at the group (or herd) level.

### Usage

```epi.pooled(se, sp, P, m, r)
```

### Arguments

 `se` a vector of length one defining the sensitivity of the individual test used. `sp` a vector of length one defining the specificity of the individual test used. `P` scalar, defining the estimated true prevalence. `m` scalar, defining the number of individual samples to make up a pooled sample. `r` scalar, defining the number of pooled samples per group (or herd).

### Value

A list containing the following:

 `HAPneg` the apparent prevalence in a disease negative herd. `HSe` the estimated group (herd) level sensitivity. `HSp` the estimated group (herd) level specificity.

### References

Dohoo I, Martin W, Stryhn H (2003). Veterinary Epidemiologic Research. AVC Inc, Charlottetown, Prince Edward Island, Canada, pp. 115 - 117 .

Christensen J, Gardner IA (2000). Herd-level interpretation of test results for epidemiologic studies of animal diseases. Preventive Veterinary Medicine 45: 83 - 106.

### Examples

```## EXAMPLE 1:
## We want to test dairy herds for Johne's disease using faecal culture
## which has a sensitivity and specificity of 0.647 and 0.981, respectively.
## Suppose we pool faecal samples from five cows together and collect six
## pooled samples per herd. What is the herd level sensitivity and specificity
## based on this approach (assuming homogenous mixing)?

epi.pooled(se = 0.647, sp = 0.981, P = 0.12, m = 5 , r = 6)

## Herd level sensitivity is 0.927, herd level specificity is 0.562.
## Sensitivity at the herd level is increased using the pooled sampling
## approach. Herd level specificity is decreased.
```

[Package epiR version 2.0.38 Index]