gtcorr.matrix.user: Calculate the efficiency of matrix group testing procedures for user specified arrangements

Description

‘gtcorr.matrix.user’ calculates the efficiencies of matrix based group testing procedures, allowing for correlation between units and test error. Cluster arrangements can are specified by the user and probability of testing postive and correlation can vary by cluster.

Usage

gtcorr.matrix.user(clusters, p, sigma=0, se=1, sp=1, model = c("beta-binomial", "Madsen", "Morel-Neerchal"))

Arguments

clusters

a matrix of integers from 1 up to the total number of clusters. cluster[i,j] is the ith, jth unit's cluster.

probability of a unit testing positive. If the length is one, then all clusters have the same probability of testing positive. If the length is the total number of clusters, then p[k] is the probability that a unit in the kth cluster tests positive.

sigma

pairwise correlation of two units in a cluster. If the length is one, then all clusters have the same pairwise correlation. If the length is the total number of clusters, then sigma[k] is the pairwise correlation for the kth cluster.

sensitivity. The probability that a pool of units tests positive given than at least one unit in that pool is positive

specificity. The probability that a pool of units tests negative given that at least one unit in that pool is negative

model

probability model for clusters. Should be ‘beta-binomial’, ‘Madsen’, or ‘Morel-Neerchal’.

Value

A length one vector containing the efficiency is returned

References

Samuel D. Lendle, Michael Hudgens, and Bahjat F. Qaqish, "Group Testing for Case Identification with Correlated Responses" Submitted 2011. Biometrics.

Examples

Run this code

##Calculate the efficiency of a 4 by 4 matrix procedure where the first
##two rows are in the first cluster, the bottom left 2 by 2 submatrix
##makes up the second cluster, and the bottom right 2 by 2 submatrix
##makes up the third cluster.
clusters <- matrix(NA, 4, 4)
clusters[1:2, ] <- 1
clusters[3:4, 1:2] <- 2
clusters[3:4, 3:4] <- 3
p <- .01
sigma <- .4
gtcorr.matrix.user(clusters, p, sigma)