Migrating from older versions

1.0 -> 1.1

HMMBase v1.1 introduces the following breaking changes:

  • viterbi(a, A, L) -> viterbi(a, A, LL) or (temporarily) viterbi(a, A, L, logl = false)

0.0.14 -> 1.0

HMMBase v1.0 introduces the following breaking changes:

  • HMM struct renaming: π0, π, D become a, A, B
  • Removal of StaticHMM and StaticArrays dependency
  • Methods renaming, see below for a full list
  • Forward/Backward algorithms uses likelihood by default (instead of log-likelihoods), use the logl option to use log-likelihoods
  • Baum-Welch algorithm returns hmm, history instead of hmm, logtot
  • rand(hmm, T) returns y instead of z, y by default, use seq = true to get z, y

Deprecated/renamed methods

# @deprecate old new

@deprecate n_parameters(hmm) nparams(hmm)
@deprecate log_likelihoods(hmm, observations) likelihoods(hmm, observations, logl = true)

@deprecate forward_backward(init_distn, trans_matrix, log_likelihoods) posteriors(init_distn, trans_matrix, log_likelihoods, logl = true)
@deprecate messages_forwards(init_distn, trans_matrix, log_likelihoods) forward(init_distn, trans_matrix, log_likelihoods, logl = true)
@deprecate messages_backwards(init_distn, trans_matrix, log_likelihoods) backward(init_distn, trans_matrix, log_likelihoods, logl = true)

@deprecate forward_backward(hmm, observations) posteriors(hmm, observations, logl = true)
@deprecate messages_forwards(hmm, observations) forward(hmm, observations, logl = true)
@deprecate messages_backwards(hmm, observations) backward(hmm, observations, logl = true)

@deprecate messages_forwards_log(init_distn, trans_matrix, log_likelihoods) log.(forward(init_distn, trans_matrix, log_likelihoods, logl = true)[1])
@deprecate messages_backwards_log(trans_matrix, log_likelihoods) log.(backward(init_distn, trans_matrix, log_likelihoods, logl = true)[1])

@deprecate compute_transition_matrix(seq) gettransmat(seq, relabel = true)
@deprecate rand_transition_matrix(K, α = 1.0) randtransmat(K, α)