BayesianTools

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Which 3PGN version was used?

3

Hi @mspeich - I am just wondering - which 3PGN version did you use for the paper? I suspect you installed checcomi/threePGN-package/r3pg but it seems Francesco transferred the project to...

florianhartig

DREAM and DREAMzs: updateInterval must be >= nCR?

1

I've found that specifying the updateInterval to be less than nCR results in an error from [line 398](https://github.com/florianhartig/BayesianTools/blob/master/BayesianTools/R/mcmcDREAMzs.R#L398) in mcmcDREAMzs.R, which is a loop over (k in 1:settings$nCR): `ind

jds485

WAIC calculations

2

add to the WAIC function the option to read in a pointwise logLikelihood matrix from another program, e.g. Jags. While at it * check that calculations are identical to WAIC...

florianhartig

lower / upper

1

lower / upper is only for the prior, can be set in createPrior createBayesianSetup -> passes this on to createPrior plotLower, plotUpper can be set for setup and is used...

florianhartig

summary() should return a list with useful values

4

currently, summary() returns the correlation matrix of the parameters, would be more sensible to return a list with all summary statistics calculated

florianhartig

Marginal likelihood - implementation of the Chib/Jeliazkov method

4

Question from a user: ich habe eine Frage zu Ihrem Rcode für die Chib/Jeliazkov Methode in der Funktion marginalLikelihood. Dort steht, dass theta.star für dmvnorm und rmvnorm als Mittelwert verwendet...

florianhartig

Numeric instability in the Twalk

8

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...

florianhartig

Pre-optimization and adaptation

3

It would be nice to have a more general concept for pre-optimization and adaptation. At the moment, only the Metropolis MCMCs do pre-optimization. The first thing I'd like to look...

florianhartig

TravisCI requires libnlopt-dev

8

TravisCI in the master branch (devel build) is failing with the warning: ``` Found file(s) with version 3 serialization: ‘build/vignette.rds’ Such files are only readable in R >= 3.5.0. Recreate...

TankredO

Possible to thin a BayesianOutput object prior to restart / -> memory problems in z-matrix

9

I wrote a loop around runMCMC to check convergence, but I am having trouble with memory errors when the BayesianOutput object grows too big after multiple calls. Is it possible...

woodwards