inst/examples/proposalGeneratorHelp.R

In BayesianTools: General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

testMatrix = matrix(rep(c(0,0,0,0), 1000), ncol = 4)
testVector = c(0,0,0,0)


##Standard multivariate normal proposal generator

testGenerator <- createProposalGenerator(covariance = c(1,1,1,1), message = TRUE)

methods(class = "proposalGenerator")
print(testGenerator)

x = testGenerator$returnProposal(testVector)
x

x <- testGenerator$returnProposalMatrix(testMatrix)
boxplot(x)

##Changing the covariance
testGenerator$covariance = diag(rep(100,4))
testGenerator <- testGenerator$updateProposalGenerator(testGenerator, message = TRUE)

testGenerator$returnProposal(testVector)
x <- testGenerator$returnProposalMatrix(testMatrix)
boxplot(x)


##-Changing the gibbs probabilities / probability to modify 1-n parameters

testGenerator$gibbsProbabilities = c(1,1,0,0)
testGenerator <- testGenerator$updateProposalGenerator(testGenerator)

testGenerator$returnProposal(testVector)
x <- testGenerator$returnProposalMatrix(testMatrix)
boxplot(x)


##-Changing the gibbs weights / probability to pick each parameter

testGenerator$gibbsWeights = c(0.3,0.3,0.3,100)
testGenerator <- testGenerator$updateProposalGenerator(testGenerator)

testGenerator$returnProposal(testVector)
x <- testGenerator$returnProposalMatrix(testMatrix)
boxplot(x)


##-Adding another function

otherFunction <- function(x) sample.int(10,1)

testGenerator <- createProposalGenerator(
  covariance = c(1,1,1), 
  otherDistribution = otherFunction, 
  otherDistributionLocation = c(0,0,0,1),
  otherDistributionScaled = TRUE
)

testGenerator$returnProposal(testVector)
x <- testGenerator$returnProposalMatrix(testMatrix)
boxplot(x)
table(x[,4])