Arrange a matrix of probabilities for informative array testing
Arrange a vector of individual risk probabilities in a matrix for informative array testing without master pooling.
Informative.array.prob(prob.vec, nr, nc, method = "sd")
prob.vec |
vector of individual risk probabilities, of length nr*nc. |
nr |
the number of rows in the array. |
nc |
the number of columns in the array. |
method |
character string defining the method to be used for matrix arrangement. Options include spiral ("sd") and gradient ("gd") arrangement. See McMahan et al. (2012) for additional details. |
A matrix of probabilities arranged according to the specified method.
This function was originally written by Christopher S. McMahan for McMahan et al. (2012). The function was obtained from http://chrisbilder.com/grouptesting.
McMahan, C., Tebbs, J., Bilder, C. (2012). “Two-Dimensional Informative Array Testing.” Biometrics, 68(3), 793–804. ISSN 0006341X, doi: 10.1111/j.1541-0420.2011.01726.x.
p.vec.func for generating a vector of individual
risk probabilities from an overall probability of disease and
Array.Measures for calculating operating characteristics
for informative array testing without master pooling.
Other Individual risk probability functions: beta.dist,
p.vec.func
# Use the gradient arrangement method to create a matrix # of individual risk probabilities for a 10x10 array. # Depending on the specified probability, alpha level, # and overall group size, simulation may be necessary in # order to generate the vector of individual probabilities. # This is done using the p.vec.func() function and requires # the user to set a seed in order to reproduce results. # This example takes less than 1 second to run. # Estimated running time was calculated using a # computer with 16 GB of RAM and one core of an # Intel i7-6500U processor. set.seed(1107) p.vec1 <- p.vec.func(p=0.05, alpha=2, grp.sz=100) Informative.array.prob(prob.vec=p.vec1, nr=10, nc=10, method="gd") # Use the spiral arrangement method to create a matrix # of individual risk probabilities for a 5x5 array. # Depending on the specified probability, alpha level, # and overall group size, simulation may be necessary in # order to generate the vector of individual probabilities. # This is done using the p.vec.func() function and requires # the user to set a seed in order to reproduce results. # This example takes less than 1 second to run. # Estimated running time was calculated using a # computer with 16 GB of RAM and one core of an # Intel i7-6500U processor. set.seed(8791) p.vec2 <- p.vec.func(p=0.02, alpha=0.5, grp.sz=25) Informative.array.prob(prob.vec=p.vec2, nr=5, nc=5, method="sd")
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