accessing pWAIC values

[Dylan Hubl]

Hi,

I am running a multispecies occupancy model and am picking up a warning that "There are 1 individual pWAIC values that are greater than 0.4...."

Trying to figure out if this is an issue that should prevent me from using WAIC as a method of model selection has been difficult. Namely, I would like to see what value is causing the warning but can't seem to figure out how to do that. 

I have searched back through old conversations in this group and found one (https://groups.google.com/g/nimble-users/c/a5ZGHVhQL34) in which it was recommended to download a new version of NIMBLE which would make it possible to view the nodes and their pWAIC values. But there was no information on what function to call to make that happen. Is it possible to use this if my code uses the one-line invocation of MCMC (e.g., nimbleMCMC())? 

Thanks,

Dylan

[Chris Paciorek]

hi Dylan,

In the conversation you found, I gave a pointer to a branch one could install NIMBLE from so that the nodes with high pWAIC are reported. It looks like that branch was based on nimble version 1.3.0. 

To update things, I've set up a new branch based on version 1.4.2 that you can install from GitHub. The branch is `report-waic-nodes-1.4.2`.

You can install from that branch like this:

```

remotes::install_github("nimble-dev/nimble", ref = "report-waic-nodes-1.4.2", subdir = "packages/nimble")

```

If you then rerun your MCMC you should see some additional output that hopefully gives you what you need (but is likely not be formatted all that cleanly).

-Chris

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[Dylan Hubl]

Hi Chris,

Thank you for the updated download. Really helpful. Is there anyway to see what the pWAIC value actually is for the problem node? Knowing how much larger than 0.4 the value is could be helpful.

Thanks,

Dylan

[Chris Paciorek]

Yes, good point. I should have added that.

I just added it to the same branch, so please reinstall and try again. 

I'm about to be out of town for a bit, so if you need to make other tweaks, such as formatting, you may be able to modify the code in MCMC_WAIC.R in the R folder of that branch and then rebuild and reinstall the package yourself.

Or I could take a look when I am back.

-chris