DBHC 0.0.4

Bug fixes

cluster.bic() passes its eps argument on to count.parameters(), it always used the default threshold before
hmm.clust() passes its smoothing argument on to assign.clusters(), cluster assignment always smoothed with the default before
smooth.probabilities() returns a uniform distribution for a set of probabilities that are all zero, which used to stay zero and is then rejected by build_hmm()
smooth.probabilities() no longer returns negative probabilities. Absolute discounting assumes the smoothing parameter is smaller than the smallest non-zero probability, and the amount discounted is now lowered to respect that. A probability below the parameter used to be discounted to a negative value, which survived because the row still sums to one, and grew more negative every time the model was smoothed again. Estimates for data with sparse emissions change, see below
select.seeds() stops with a message when too few sequences are left to fill a seed, it used to select NA ids
Loops over sequences and cluster models use seq_along(), they could run an iteration on an empty set

Sequences are evaluated against a cluster model all at once in assign.clusters() and select.seeds() instead of one at a time, which makes the algorithm about five times faster on 1000 sequences and leaves all results unchanged
hmm.clust() has an argument max.iter and size.search() has an argument max.states to bound the search for cluster memberships and hidden states
An infeasible HMM raises a warning instead of printing one
The smaller Swiss Household example is fast enough to run on test again
Both Swiss Household examples are wrapped in \donttest instead of \dontrun, they are slow rather than impossible to run
Results for data with sparse emission probabilities change slightly because of the fix to smooth.probabilities() above. On the simulation study of the accompanying paper nothing changes but the BIC, by 0.0001 percent. On the full Swiss Household data the cluster models and a small number of cluster memberships change, the number of clusters and their sizes do not

Replaced Author and Maintainer with Authors@R
Dropped LazyData, the package has no data directory
Requires seqHMM (>= 2.0.0), the version this release is tested against
Heatmaps refer to their data with the .data pronoun, which silences the deprecation warnings from ggplot2