NEWS
seqHMM 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 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 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 2022-12-13
- Changed the internal seqplot axes argument to xaxis as axes is now
deprecated in TraMineR.
seqHMM 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 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 2021-10-18
- seqHMM now supports fixed values in initial, transition, and emission
probabilities when performing model estimation.
seqHMM 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 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 2019-10-21
- Added an option for defining legend labels and colours manually in plot.hmm.
seqHMM 2019-06-11
- Fixed a bug when calling plot.mhmm inside a function. Thanks to Ellen Graham for
catching the issue.
seqHMM 2019-04-11
- Fixed an OpenMP sharing issue due to upcoming GCC9.
seqHMM 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 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 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 2018-05-03
- Fixed encoding issues in references.
- Updated author affiliations.
seqHMM 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 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 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 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 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 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 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 2015-12-19
First version on CRAN.