Comments (2)
It's bit hard to know exactly what is wrong without reproducible example, but lie the error messages say, your emission matrix has to contain all the symbols which occur in the data, and potentially some extra symbols as well though if you just define the alphabet of the stslist object accordingly. See this:
library(seqHMM)
set.seed(1)
k <- 3
s <- 10 # ten symbols
# say A and B are from training data
A <- matrix(runif(k^2), k, k)
A <- A / rowSums(A)
B <- matrix(runif(k*s),k,s)
B <- B / rowSums(B)
# new data, define the same alphabet (set of symbols)
y<-seqdef(t(sample(1:7,size=100,replace=TRUE)),alphabet=1:10) # note the alphabet argument
model <- build_hmm(y, trans=A, emiss=B, init=c(1,0,0))
logLik(model)
from seqhmm.
alphabet=1:10) # note the alphabet argument
Thank You very much for your help. Lack of alphabet caused problems, now it works.
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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from seqhmm.