Hey guys - What’s the easiest way to read cmdstan into R from optimization output (I can use linux or some for loops), But more important: how can I just dump my dev stan math into Rstan? I’m using some of my own functions (i.e. kernels) that aren’t available in Rstan, so I’m need to make my Rstan …

I think R’s read.csv should work.

Isn’t it just a CSV file with some comments? What do you need out of it?

I just need the point estimates for hyper parameters, and then the predictive distributions. I can sed away at it or with a simple python script. This isn’t too much of an issue. More important is getting the dev into RStan (or may be pystan). I’ll have a look at part 1 right now.

Just read in the CSV file, then. It will have a header for parameter names and values for the iterations, I think.

[image] Rstan::read_stan_csv chokes on NaN RStan For some reason rstan will not let me load output files with NaN values (which happen because the model program covers a variety of model types and outputs some irrelevant values). Is there a flag to create the object any…

it’s pretty simple actually, just a little obnoxious, for optimization I need to extract the output and write stan code to re calculate the kernel and predictive distribution with the point estimates. This is probably not making me look professional, just gambling with time really, this is process i…

wow! overlooking simple things, every day!

cmdStan output to R, or dev branch in Rstan

Developers

anon79882417 July 25, 2018, 9:18pm 5

has to do with this issue. it doesn’t like nan and quantiles are irrelevant in this setting when we’re using MAP (i think with BFGS we’re optimizing parameters jointly, is MAP the correct way to think about this?).

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cmdStan output to R, or dev branch in Rstan

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