epiR (version 0.9-32)

epi.prev: Estimate true prevalence

Description

Computes the true prevalence of a disease in a population on the basis of an imperfect test.

Usage

epi.prev(pos, tested, se, sp, conf.level = 0.95)

Arguments

pos

the number of positives.

tested

the number tested.

se

test sensitivity (0 - 1).

sp

test specificity (0 - 1).

conf.level

magnitude of the returned confidence interval. Must be a single number between 0 and 1.

Value

• A list containing the following:
• ap
  the point estimate of apparent prevalence, the standard error of the apparent prevalence, and the lower and upper bounds of the confidence interval around the apparent prevalence estimate.
• tp
  the point estimate of the true prevalence, the standard error of the true prevalence, and the lower and upper bounds of the confidence interval around the true prevalence estimate.

Details

Exact binomial confidence limits are calculated for apparent prevalence (see Collett 1999 for details).

References

Abel U (1993). DieBewertung Diagnostischer Tests. Hippokrates, Stuttgart. Collett D (1999). Modelling Binary Data. Chapman & Hall/CRC, Boca Raton Florida, p. 24. Gardener IA, Greiner M (1999). Advanced Methods for Test Validation and Interpretation in Veterinary Medicince. Freie Universitat Berlin, ISBN 3-929619-22-9; 80 pp. Messam L, Branscum A, Collins M, Gardner I (2008) Frequentist and Bayesian approaches to prevalence estimation using examples from Johne's disease. Animal Health Research Reviews 9: 1 - 23. Rogan W, Gladen B (1978). Estimating prevalence from results of a screening test. American Journal of Epidemiology 107: 71 - 76.

Examples

## A simple random sample of 150 cows from a herd of 2560 is taken.
## Each cow is given a screening test for brucellosis which has a 
## sensitivity of 96\% and a specificity of 89\%. Of the 150 cows tested
## 23 were positive to the screening test. What is the estimated prevalence 
## of brucellosis in this herd (and its 95\% confidence interval)?

epi.prev(pos = 23, tested = 150, se = 0.96, sp = 0.89, conf.level = 0.95)

## The estimated true prevalence of brucellosis in this herd is 5.1 cases per 
## 100 cows (95\% CI 0 -- 12 cases per 100 cows).