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florianhartig
Numeric instability in the Twalk
There is a numeric problem in the T-walk. For the simple test densities this did not occur, but for the VSEM, if I run the following example, the algorithm jumps sometimes into areas of the posterior space that are practically impossible in terms of the log posterior differences.
I suspect that there is somewhere some under/overflow issue in the jump probabilities, maybe in the g function, but I didn't see an obvious problem so far.
library(BayesianTools)
PAR <- VSEMcreatePAR(1:1000)
refPars <- VSEMgetDefaults()
refPars[12,] <- c(2, 0.1, 4)
rownames(refPars)[12] <- "error-sd"
head(refPars)
referenceData <- VSEM(refPars$best[1:11], PAR)
referenceData[,1] = 1000 * referenceData[,1]
obs <- referenceData + rnorm(length(referenceData), sd = refPars$best[12])
parSel = c(1:6, 12)
likelihood <- function(par, sum = TRUE){
x = refPars$best
x[parSel] = par
predicted <- VSEM(x[1:11], PAR) # replace here VSEM with your model
predicted[,1] = 1000 * predicted[,1] # this is just rescaling
diff <- c(predicted[,1:4] - obs[,1:4]) # difference betweeno observed and
llValues <- dnorm(diff, sd = x[12], log = TRUE)
if (sum == FALSE) return(llValues)
else return(sum(llValues))
}
bayesianSetup <- createBayesianSetup(likelihood, lower = refPars$lower[parSel], upper = refPars$upper[parSel], names = rownames(refPars)[parSel])
settings <- list(iterations = 200000, nrChains = 1)
out <- runMCMC(bayesianSetup = bayesianSetup, sampler = "Twalk", settings = settings)
plot(out, parametersOnly = F, which = c(1:7,9), start = 2000)
x = getSample(out, parametersOnly = F, which = c(1:7,9), start = 2000)
low = which(x[,8] < -9000)
apply(x[low,],2,mean)
likelihood(x[low[1],1:7])
x[low[1],8]
This seems to be more complicated, added a warning in https://github.com/florianhartig/BayesianTools/commit/1bb636af652129ce7276c2fb244b059fdddf7abf
I checked the Rtwalk package and the same problem occurs there, maybe it would be better/faster to rewrite the whole sampler
is our code comparable in structure to this package? Because when I remember correctly, @stefan-paul had implemented it differently than the code from the publication ...
A colleague told me that he had the feeling the https://cran.r-project.org/web/packages/Rtwalk/index.html package works - could you try out if the sampler in the T-walk package works where ours fails?
Sorry, I just saw that Max had already tried this - but maybe try if this is still so. Also, we should maybe tell the guys that they have a problem in their package!
Did anyone check the sampler in the original paper? If I remember correctly, there was code included with the paper!
@JohannesOberpriller - when I looked at the code, I was relatively sure the problem is in the Gfun (if I remember correctly, or one of the helper functions) - the weird jumps occur when one of these functions creates very high values. Didn't look like an overflow though, seemed the values were realistic!