Description Usage Arguments Value Examples
Fit an empirical Bayes prior to the data
1 2 | empiricalBayesPrior(datasets, distributions = "diagNormal",
globalConcentration = 0.1, localConcentration = 0.1, type = "fitRate")
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datasets |
List of data matrices where each matrix represents a context-specific dataset. Each data matrix has the size N times M, where N is the number of data points and M is the dimensionality of the data. The full list of matrices has length C. The number of data points N must be the same for all data matrices. |
distributions |
Distribution of data in each dataset. Can be either a list of
length C where |
globalConcentration |
Prior concentration parameter for the global clusters. Small values of this parameter give larger prior probability to smaller number of clusters. |
localConcentration |
Prior concentration parameter for the local context-specific clusters. Small values of this parameter give larger prior probability to smaller number of clusters. |
type |
Type of prior that is fitted to the data. The algorithm can fit either rate of the prior covariance matrix, or fit the full covariance matrix to the data. |
Returns the prior object that can be used as an input for the contextCluster
function.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | # Example with simulated data (see vignette for details)
nContexts <- 2
# Number of elements in each cluster
groupCounts <- c(50, 10, 40, 60)
# Centers of clusters
means <- c(-1.5,1.5)
testData <- generateTestData_2D(groupCounts, means)
datasets <- testData$data
# Generate the prior
fullDataDistributions <- rep('diagNormal', nContexts)
prior <- empiricalBayesPrior(datasets, fullDataDistributions, 0.01, 0.1, 'fitRate')
# Fit the model
# 1. specify number of clusters
clusterCounts <- list(global=10, context=c(3,3))
# 2. Run inference
# Number of iterations is just for demonstration purposes, use
# a larger number of iterations in practice!
results <- contextCluster(datasets, clusterCounts,
maxIter = 10, burnin = 5, lag = 1,
dataDistributions = 'diagNormal', prior = prior,
verbose = TRUE)
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