Open drnickisaac opened 3 years ago
This is failing five separate tests of bma()
, where it's expecting the results to equal certain specific values. I thought it was due to the hyperprior changes, but I reverted locally and the same error trips. So I'm wondering if this is related to a change in the RNG, as happened in sparta.
https://github.com/BiologicalRecordsCentre/sparta/issues/219
What do you think @AugustT ?
error relate to checks of BMA, looks like output values don't quite match the expected.
@drnickisaac I think you might be right. Smells like the same problem we had with sparta. That seemed to be an R version or OS issue with random number generation. This is an on-going problem but I can't think of a better test. Hopefully we can fix this here and they wont mess with the random number generators in the future
While you are at it did you see the warnings about seed?
��� Warning (testbma.R:17:3): simple run ────────────────────────────────────────
The 'seed' argument will be deprecated in the next version. You can set it yourself with set.seed() instead.
Backtrace:
1. BRCindicators::bma(...) testbma.R:17:2
2. jagsUI::jags(...)
3. jagsUI:::process.input(...)
4. jagsUI:::gen.inits(inits, n.chains, seed, parallel)
We should change to use set.seed() rather than the seed argument to JAGS. 2 birds 1stone.
@AugustT I think it is related to this discussion about Mac vs Windows errors. and this one too.
It looks like you fixed it in a PR to my branch on 5th Feb. It looks like the fix was as simple as adding set.seed(125)
before every example, rather than just the first one.
I've looked at testbma
: all but one of the tests already had the seed set explicitly, so that can't explain the multiple failures seen on Travis.
Any ideas @AugustT ?
I think in the sparta case I was able to replicate the error on my PC and then use the new numbers to update my test. I dont think I have done that for the BRCindicators case
I cant get the random number stuff fixed. Sparta uses R2jags, BRCindicators uses JAGSui, that is the only thing I can see that explains the difference. For now I think we will have to remove this test.
I get a few warnings At least one Rhat value could not be calculated.
I assume this is because the test dataset is so small?
No: that's because the first year estimate is a fixed number, so no variatuon among chains.
On Mon, 29 Mar 2021, 10:32 Dr Tom August, @.***> wrote:
I get a few warnings At least one Rhat value could not be calculated. I assume this is because the test dataset is so small?
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Oh right, is that a warning we should handle then?
Ideally, yes. It would be great if that warning were suppressed. It is entirely to be expected, but potentially alarming for a naive user. Nick
On Mon, 29 Mar 2021 at 21:38, Dr Tom August @.***> wrote:
Oh right, is that a warning we should handle then?
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It seems like travis tests are no longer working @robboyd was going to look into alternatives
@JimBacon is investigating Travis replacement options for Indicia. You can probably stick with Travis as this work is non-commercial? https://github.com/Indicia-Team/warehouse/issues/375
We found a problem whereby 0 was included in the prior range of
sd
parameters: when converted into precisions, this permitsInf
to be included in the distribution of precision parameters, thus causing fail in JAGS. Fix is to add a small number to the hyperpriors. A few other documentation issues fixed