Nothing
bpec.covariatesPlot = function(bpecout, colorCode = c(7,5,6,3,2,8,4,9)) {
writeLines("Creating covariate distribution plot...")
covNames = colnames(bpecout$input$coordsLocs)
meanSamples = bpecout$clust$sampleMeans
covSamples = bpecout$clust$sampleCovs
noClusters=dim(meanSamples)[2]
dims=dim(meanSamples)[1]
subSeq=seq(1, length(covSamples[1, 1, 1, ]), length.out = 20)
meanSamplesSub = meanSamples[, , subSeq]
fullClust = numeric(noClusters)
for(i in 1:noClusters) {
if (length(which(!is.na(meanSamplesSub[1, i, ]))) > 0) {
fullClust[i] = 1
} else {
fullClust[i] = 0
}
}
if (dims > 2) {
for(i in 3:dims) {
# w=seq(min(Means[i,])-2*max(sqrt(Covs[i,i,])),max(Means[i,])+2*max(sqrt(Covs[i,i,])),length=100)
# w=seq(min(MeanSamples[i,,],na.rm=TRUE)-2*max(sqrt(CovSamples[i,i,,]),na.rm=TRUE),max(MeanSamples[i,,],na.rm=TRUE)+2*max(sqrt(CovSamples[i,i,,]),na.rm=TRUE),length=100)
# w=seq(min(MeanSamples[i,,],na.rm=TRUE)-1*mean(sqrt(CovSamples[i,i,,]),na.rm=TRUE),max(MeanSamples[i,,],na.rm=TRUE)+1*mean(sqrt(CovSamples[i,i,,]),na.rm=TRUE),length=100)
w=seq(mean(meanSamples[i, , ], na.rm = TRUE) - 3 * mean(sqrt(covSamples[i, i, , ]), na.rm = TRUE), mean(meanSamples[i, , ], na.rm = TRUE) + 3 * mean(sqrt(covSamples[i, i, , ]), na.rm = TRUE), length = 100)
maxax = 0
for(j in 1:noClusters) {
if (fullClust[j] == 0) {
next
}
for(it in 1:dim(meanSamples)[3]) {
if (is.na(meanSamples[i, j, it]) == FALSE) {
dnst = dnorm(w, meanSamples[i, j, it], sqrt(covSamples[i, i, j, it]))
if (max(dnst) > maxax) {
maxax = max(dnst)
}
}
}
}
plot(w, dnst, col='white', ylim = c(0, maxax), type = 'l', xlab = covNames[i], ylab = "")
for(j in 1:noClusters) {
if (fullClust[j] == 0) {
next
}
densIt = array(NA, dim = c(length(w), dim(meanSamples)[3]))
for(it in 1:dim(meanSamples)[3]) {
if (is.na(meanSamples[i, j, it]) == FALSE) {
densIt[, it] = dnorm(w, meanSamples[i, j, it], sqrt(covSamples[i, i, j, it]))
}
}
densUp = w
densLow = w
densMed = w
for(jj in 1:length(w)) {
densUp[jj] = quantile(densIt[jj, ], 0.9, na.rm = TRUE)
densLow[jj] = quantile(densIt[jj, ], 0.1, na.rm = TRUE)
densMed[jj] = quantile(densIt[jj, ], 0.5, na.rm = TRUE)
}
colCont = col2rgb(colorCode[j], alpha = FALSE)
polygon(c(w, rev(w)), c(densLow, rev(densUp)), col = c(rgb(colCont[1] / 255, colCont[2] / 255, colCont[3] / 255, alpha = 0.3)), border = NA)
lines(w, densMed, col = colorCode[j])
}
}
}
}
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