seqHMM 1.2.6 (Release
date: 2023-06-07)
- Armadillo solver now fails directly instead of trying approximate
solution in case of numerical issues when estimating the regression
coefficients.
build_mm now correctly runs EM algorithm only in case
of real missing observations in data, i.e. it correctly handles void
values.
seqHMM 1.2.5 (Release
date: 2023-06-13)
- New methods
state_names and cluster_names
for getting and setting state and cluster names of the model
objects.
- Fixed a bug in
mssplot which caused error with
respect_void = TRUE.
- Fixed a bug in
simulate_mhmm which resulted NA colnames
in the simulated stslist objects.
- Modified internals of
ssp to be compatible with the
latest versions of TraMineR.
- The
data argument is no longer optional if
formula is used in build_mhmm,
build_mmm and build_lcm functions.
- Added few unit tests using testthat.
seqHMM 1.2.4 (Release
date: 2023-01-09)
- Fixed the issue with the initial transition matrix construction in
build_mm when there is a symbol which is only present in last time
points.
- Related to above, if a state x with no transitions from is
encountered during the EM algorithm, the corresponding row of the
transition matrix A is then normalized so that is such a A[x,x]=1
i.e. the state is set as absorbing.
seqHMM 1.2.3 (Release
date: 2022-12-13)
- Changed the internal seqplot axes argument to xaxis as axes is now
deprecated in TraMineR.
seqHMM 1.2.2 (Release
date: 2022-12-01)
- Fixed the handling of models with more than 200 symbols in mc_to_sc,
mc_to_sc_data, and plotting functions.
- Removed duplicate xaxis argument in interal SSPlotter function.
seqHMM 1.2.1-1 (Release
date: 2022-05-24)
- Added argument respect_void to hidden_paths function leading to the
propagation of void values of observed sequences to the hidden state
sequences.
- Fixed the scaling of initial probabilities to 1 in build_mm.
- Fixed the computation of the initial state probability vector for
Markov models in case of missing data.
seqHMM 1.2.0 (Release
date: 2021-10-18)
- seqHMM now supports fixed values in initial, transition, and
emission probabilities when performing model estimation.
seqHMM 1.1.1 (Release
date: 2021-08-13)
- Fixed a a case with the equality constraints which resulted an error
during the estimation in case of (numerically) nonfinite parameter
value.
- Function fit_model now checks whether the initial model produces
finite likelihood before proceeding further.
seqHMM 1.1.0 (Release
date: 2021-06-18)
- Added a feature which allows equality constraints for emission
probability distributions.
- Fixed the documentation of biofam3c data.
- Added a check for degenerate model for ‘fit_model’ where one
channels contains only missing values.
seqHMM 1.0.14 (Release
date: 2019-10-21)
- Added an option for defining legend labels and colours manually in
plot.hmm.
seqHMM 1.0.13 (Release
date: 2019-06-11)
- Fixed a bug when calling plot.mhmm inside a function. Thanks to
Ellen Graham for catching the issue.
seqHMM 1.0.12 (Release
date: 2019-04-11)
- Fixed an OpenMP sharing issue due to upcoming GCC9.
seqHMM 1.0.11 (Release
date: 2019-04-09)
- All functions relying on C++ are now slightly faster due to more
efficient data transformations from factors to integers.
- Fixed an OpenMP sharing issue due to upcoming GCC9.
seqHMM 1.0.10 (Release
date: 2019-01-25)
- Fixed iteration counter for EM algorithm, now maxeval=1 actually
does one iteration and not two. Similarly fixed the the corresponding
printing of intermediate results.
- build_hmm and build_hmm now ignore n_states argument if any of the
initial values are provided.
- Updated some formulas in the algorithms vignette to correspond to
current forward-backward variant.
- Updated citation info due to the publication in JSS.
seqHMM 1.0.9 (Release
date: 2018-11-06)
- Fixed a bug in backward and posterior probabilities of multivariate
models stemming from changes in version 1.0.7, causing the incorrect
scaling factors. Note that issue was only in forward_backward and
posterior_probs functions with log_scale = FALSE, internally the package
still used correct implementations when calling fit_model. Thanks for
Silvia Bacci for noticing the issue.
- Fixed OpenMP flags in Makevars.
seqHMM 1.0.8-1 (Release
date: 2018-05-03)
- Fixed encoding issues in references.
- Updated author affiliations.
seqHMM 1.0.8 (Release
date: 2017-11-07)
- Fixed a bug in forward_backward function, which did not provide
correct scaling factors for last time point and thus the backward
variables weren’t F scaled correctly.
- Related to above bug, posterior_probs now provides proper
probabilities between 0 and 1.
- Fixed a bug in ssp; caused an error for sortv = “hidden.paths” when
hidden paths were not provided even though x was an hmm object.
- Changed argument withlegend to with.legend due to changes in the
TraMineR package.
- Related to the TraMineR update, fixed warnings given by ssp
functions.
- Fixing model plots after an update in the igraph package.
seqHMM 1.0.7 (Release
date: 2017-04-04)
- Added supplementary vignettes for visualization, estimation, and
theoretical background.
- Corrected a “feature” of the scaled forward-backward algorithm which
caused potential numerical issues in backward probabilities. More
specifically, previously the scaled backward variable at time t was
scaled with the scaling factors c_[t+1] of the forward variable, instead
of c_t. In typical applications this did not cause any problems, but
some models which previously caused problems can work now without
resorting to the log-space algorithm.
- Scaling factors used in forward-backward algorithms are now stored
as 1/c_t, where c_t are the scaling factors from older versions of
seqHMM.
- The build_mm function now automatically estimates model parameters
from the observed initial state distribution and transition counts.
- Added automatic starting values for build_hmm, build_mhmm,
build_mmm, and build_lcm.
Bug fixes:
- Fixed a bug from version 1.0.6 where the EM algorithm with restarts
did not work as efficiently as intended due to changes in initializing
emission matrices. More specifically, the previous version used Rcpp
sugar which does not use deep copies in case of arma::cubes, which
resulted the subsequent EM runs to depend on the first optimum
(affecting especially the identification of non-zero emission
probabilities).
- Fixed a bug in the ssp function where tlim was taken account of
after sorting sequences and computing hidden paths (now cases are chosen
before other actions).
seqHMM 1.0.6 (Release
date: 2016-08-01)
- Argument diag_c in simulate_transition_probs is now used also in
cases where left_right = FALSE.
- Adjusted reltol and maxeval values for EM algorithm. Now reltol is
1e-10 (previously 1e-12), and the reltol and maxeval values for restarts
are by default taken from the initial EM algorithm (previosly reltol was
1e-8 and maxeval = 100 for restarts).
- Fixed hidden states labels for ssp functions (previously always used
the default values).
Bug fixes:
- The ssplot function assigned wrong colors for hidden states in cases
where the state names were not alphabetically ordered. The performance
of the function was also improved by removing extra calls to
seqdef.
- Changing the missing.color argument did not work in legends of ssp,
ssplot, and mssplot.
- The mssplot function now works with unique hidden state names
(problem occured e.g. with latent class models).
- The mssplot function with sortv = “mds.hidden” produced strange
errors when plotting clusters with one hidden state. Now automatically
uses “mds.obs” in such cases.
seqHMM 1.0.5 (Release
date: 2016-02-24)
Bug fixes:
- The mssplot function now uses hidden paths instead of posterior
probabilities to determine the most probable cluster for each subject
(previous solution caused errors when posterior probabilities suggested
a different cluster than hidden paths).
- In mssplot, removed a misplaced tlim which caused a warning when
plotting state distributions of hidden paths.
- The gridplot function now uses with.missing.legend also with
combined legends.
seqHMM 1.0.4 (Release
date: 2016-01-14)
- Added examples for build_mmm.
- Added more space for main titles in plot.mhmm.
- Improved documentation.
- Added tlim in ssp functions.
Bug Fixes:
- Corrected mc_to_sc for single state models due to dimension
dropping.
- Corrected a bug in plot.hmm when layout = “vertical”.
- Fixed legend layout in plot.hmm.
- Wrong nobs and df attributes in mc_to_sc.
- Wrong number of sequences to ssp titles when tlim is used.
- EM with HMM using log-space produced error due to missing element in
output of EM.
seqHMM 1.0.3-1 (Release
date: 2015-12-29)
As requested by CRAN, changed donttest example of interactive
plotting to conditional block depending on whether session is
interactive or not.
seqHMM 1.0.3 (Release
date: 2015-12-23)
Corrected dependency on R 3.2.0 due to lengths function.
Bug Fixes:
- Corrected a bug which caused fit_model to stop if restarted EM
failed.
- vcov.mhmm produced errors in valgrind, corrected issue by replacing
Armadillo’s inv_sympd function with inv.
- Corrected a bug relating to colorpalette in mc_to_sc function.
Performance improvements:
- Slight performance improvement in all functions by tweaking the
usage of armadillo constructors.
seqHMM 1.0.2-1 (Release
date: 2015-12-19)
First version on CRAN.