User-visible changes only. For internal changes, see Github commits.
Fix of a bug in the Viterbi algorithm for the calculation of the fitted state at the initial time for each subject.
Bug fix for pmatrix.piecewise.msm given just intensity matrices instead of a fitted model.
Auto-generated initial values set to a small positive number rather than zero when there are no observed data for a particular permitted transition. This fixes consistency checks (e.g. for qconstraint) in this situation.
Fix when covariates come into the data as one-column matrices instead of vectors.
Modernised to use roxygen, and pkgdown website created at https://chjackson.github.io/msm
Some internal functions (e.g. deriv.msm) that clash with base S3 generics renamed
rpexp is now more efficient. Thanks to Mark Clements. Note that the values simulated by rpexp, sim.msm and simmulti.msm for a specific seed will now be different in models where the intensities are piecewise constant.
Bug fix: in HMMs with partially known initial states specified through obstrue and censor, initprobs is now accounted for.
Bug fix for bootstrapping with character subject IDs.
crudeinits.msm handled when state is a factor.
Fix for hranges on multiple parameters.
obstrue handled in forward-backward algorithm (viterbi.msm).