Comments (4)
This sounds really weird. We do not define BIC
function at all, instead we rely on the default BIC method of stats
(stats:::BIC.default
), which in turn calls the logLik
method of hmm
object which returns the necessary constants for BIC as attributes. All I can think of is that you have something extra in your environment when running R from shell, like old workspace which defines own BIC.default
function, or some other package is loaded with same class name or something?
from seqhmm.
Hmmmm I think you are right, probably some of the previous packages I was using to fit HMMs might override the function...Still, I do not understand why it works in RStudio. I will check it and post it here asap.
Thanks a lot!
from seqhmm.
Finally, my problem was not exactly on the BIC function, but on the logLik function inside, which I can only link correctly from Rstudio. As a temporal workaround, I have overriden the BIC.default function and make it call explicitly to seqHMM:::logLik
from seqhmm.
I still don't understand how you can have different behaviour with Rstudio and shell if both have same R version at the background with clean workspace... Quick search at R source does not find any bits of code with log(object$K)
either...
from seqhmm.
Related Issues (20)
- [Help request] How to test the model? HOT 1
- can this package support Multivariate Discrete HMM?? HOT 3
- will it work for multivariate time series prediction : different continues or/and discrete/category observation HOT 4
- HMM cluster assignments HOT 2
- seqdata should be a state sequence object HOT 1
- Apply to financial time series? HOT 1
- Parsing HMMER3 files HOT 2
- 'System seems singular' and 'EM algorithm failed' for Mixture Markov Model HOT 2
- Building a model with different sequence lengths HOT 1
- hidden_paths does not respect sequence length HOT 4
- Parallel computation HOT 2
- Forward probability of MHMM vs HMM HOT 1
- standard errors for HMM parameters HOT 3
- Maximum number of colours in cpal/colorpalette HOT 4
- Extracting combinations of emitted states HOT 4
- Error in if (em.con$reltol < resEM$change) { : argument is of length zero HOT 5
- Absorbing state broken in `build_mm()` (seqhmm 1.2.1-1) HOT 1
- Runtime Estimation HOT 1
- EM algorithm failed HOT 1
- Error: number of labels must equal number of states in the alphabet HOT 4
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