NEWS

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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 (previously 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 occurred 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.

seqHMM 2.2.0 (2026-03-16)

• EM algorithm for NHMMs now supports SQUAREM acceleration (Varadhan and Roland, 2008).
  • Exposed argument save_all_solutions in estimate_nhmm and estimate_mnhmm for saving solutions from all restarts.
  • Changed the options of the plots argument options of stacked_sequence_plot to observations and hidden states.
  • Added an argument ids for get_*_probs functions.
  • estimate_nhmm and estimate_mnhmm now set init_sd=0 if restart=0 and user has provided initial values.
  • Added default values for id and time for stslist_to_data.
  • Fixed the forward weighting in get_marginals.
  • Improved the performance of posterior_probs.
  • Improved the performance of summary_mnhmm and computation of posterior cluster probabilities in general.
  • Improved the performance of creating the design matrices in model building.
  • Fixed a bug in coef.mnhmm which resulted an error on extracting confidence intervals for emission probabilities.
  • Fixed mnhmm example in estimate_mnhmm documentation.
  • Fixed a memory leak in the M-step of initial probabilities of NHMMs.

seqHMM 2.1.0 (2025-09-25)

• Identifiability check via QR decomposition for the design matrices can now be controlled via argument check_rank. Default is NULL, which will evaluate as TRUE if the number of sequences is at most 1000. Also, even if checks are done, they now use precomputed QR instead of doing it again.
  • Added dependency on package collapse, which resulted in much more efficient construction of non-homogeneous HMM objects.
  • Removed data.table progress printing from internal functions. Because of this recent feature, data.table version requirement is increased.
  • Fixed an issue with dropping the first time point in case where this lead to an unused factor level and subsequent error about multicollinearity.
  • Fixed the error messages regarding the missing values in covariates.
  • Fixed a typo in simulate_nhmm which caused an error in accessing elements of initial values.
  • Fixed the bug in simulate_nhmm and simulate_mnhmm which caused the covariate matrices of the returned model to be incorrect. This had no effect on the simulated observations and states though.
  • Unused factor levels are now not dropped in the simulation functions, whereas whether to drop them in estimation functions can be controlled via argument drop_levels (which is TRUE by default).
  • Fixed the column name from state_to to state in the marginal state predictions output of predict().
  • Fixed the check for valid ids argument in stacked_sequence_plot.
  • Fixed the usage of the group argument in stacked_sequence_plot.
  • Reverted the default argument log_space of fit_model and other relevant functions back to FALSE, as was the case before package version 2.0.0. Algorithms of NHMM models also now use scaling instead of log-space computations for improved speed.
  • Improved numerical stability and computational efficiency of several C++ functions related to non-homogenous models.
  • Resaved the leaves data as normal data.frame (instead of tibble).

seqHMM 2.0.0 (2025-05-16)

• Added support for non-homogeneous HMMs (NHMMs) where initial, transition, and emission probabilities can depend on individual-specific covariates. For mixture NHMMs cluster probabilities can also depend on covariates.
  • Added support for feedback-augmented NHMMs where responses and states can depend also on the past responses.
  • Added bootstrap_coef bootstrapping coefficients of NHMMs.
  • Added a function predict, which can be used to compute average marginal predictions for NHMMs, which can be interpreted as average causal effects under suitable assumptions (https://arxiv.org/abs/2503.16014).
  • Added get_* functions for obtaining initial, transition, emission and cluster probabilities and their (conditional) marginals.
  • Rewrote all post-estimation functions such as hidden_paths and forward_backward so that they return data.table.
  • Added functions stslist_to_data and data_to_stslist to convert between data frames and TraMineR's stslist objects (created by seqdef).
  • Rewrote sequence visualization functions using ggseqplot and patchwork packages. Old plotting functions are deprecated and will be removed in the future.
  • Warning and error messages were rewritten using cli package.
  • Removed the function estimate_coef. A portion of the code was accidentally commented out, rendering the function non-functional for several years. Rather than correcting the code, the function was removed as it was deemed unnecessary.
  • Added automatic tests using testthat package.
  • Internally switched from Rd syntax to Markdown in Roxygen documentation.