PooledInfRate: Estimation from pooled or group testing.
Current version: 1.6
The website for this project is https://github.com/CDCgov/PooledInfRate.
PooledInfRate is an R package that includes functions to estimate proportions from pooled or group testing data. There is also functionality to estimate differences of such proportions. Finally, for entomologists, there is functionality to compute the so-called “Vector Index” used to quantify the level of pathogen in vector species, such as the amount of West Nile virus in a population of vector mosquitoes.
You can install PooledInfRate from GitHub:
# To install from GitHub
# This will build on the fly, so you need *RTools* (available from CRAN)
Sys.setenv(R_QPDF="true") # to build the vignette during the package build
library(devtools) # need to install this if you do not have it
devtools::install_github("https://github.com/CDCgov/PooledInfRate",build_vignettes = TRUE)For those on Microsoft Windows, the binary build for version #.# is available in the file list as PooledInfRate_#.#.zip, and you can download and install that instead of the build-install. The various versions are available for Windows, as stored here.
A couple of basic examples with contrived data:
library(PooledInfRate)
## basic example code
x <- c(1,0,0,0)
m <- c(50,25,10,5)
pooledBin(x,m)
#> P Lower Upper
#> 1 0.01257911 0.0007261606 0.07828496
pool.dat <- data.frame(Pos = c(1,1,0,0), PoolSize = c(100,50,25,10), NumPools = c(5,8,2,3))
pooledBin(Pos ~ PoolSize, data = pool.dat)
#> P Lower Upper
#> 1 0.01602751 0.002879876 0.08708547
pIR(Pos ~ PoolSize + n(NumPools), data = pool.dat) # pIR is just a short name for 'pooledBin'
#> P Lower Upper
#> 1 0.00212917 0.0003860092 0.007107271See the package vignette for detailed examples of the methods and user interface, along with references for the methods.
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