rsu.sep.rspool {epiR} | R Documentation |
Calculates the surveillance system (population-level) sensitivity and specificity for detection of disease assuming representative sampling and allowing for imperfect sensitivity and specificity of the pooled test.
rsu.sep.rspool(r, k, pstar, pse, psp = 1)
r |
scalar or vector representing the number of pools. |
k |
scalar or vector of the same length as |
pstar |
scalar or vector of the same length as |
pse |
scalar or vector of the same length as |
psp |
scalar or vector of the same length as |
A list comprised of two elements:
se.p |
scalar or vector, the surveillance system (population-level) sensitivity estimates. |
sp.p |
scalar or vector, the surveillance system (population-level) specificity estimates. |
Christensen J, Gardner I (2000). Herd-level interpretation of test results for epidemiologic studies of animal diseases. Preventive Veterinary Medicine 45: 83 - 106.
## EXAMPLE 1: ## To confirm your country's disease freedom status you intend to use a test ## applied at the herd level. The test is expensive so you decide to pool the ## samples taken from individual herds. If you decide to collect 60 pools, ## each comprised of samples from five herds what is the sensitivity of ## disease detection assuming a design prevalence of 0.01 and the sensitivity ## and specificity of the pooled test equals 1.0? rsu.sep.rspool(r = 60, k = 5, pstar = 0.01, pse = 1, psp = 1) ## This testing regime returns a population-level sensitivity of disease ## detection of 0.95. ## EXAMPLE 2: ## Repeat these calculations assuming the sensitivity of the pooled test ## equals 0.90. rsu.sep.rspool(r = 60, k = 5, pstar = 0.01, pse = 0.90, psp = 1) ## If the sensitivity of the pooled test equals 0.90 the population-level ## sensitivity of disease detection is 0.93. How can we improve population- ## level sensitivity? Answer: include more pools in the study. rsu.sep.rspool(r = 70, k = 5, pstar = 0.01, pse = 0.90, psp = 1) ## Testing 70 pools, each comprised of samples from 5 herds returns a ## population-level sensitivity of disease detection of 0.95.