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Showing content from http://cran.rstudio.com/web/packages/uwot/../Rcpp/../RcppUUID/../Rcpp/../seqHMM/news/news.html below:

NEWS

• 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.

• 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.

• 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.

• 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.

• Changed the internal seqplot axes argument to xaxis as axes is now deprecated in TraMineR.

• 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.

• 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 now supports fixed values in initial, transition, and emission probabilities when performing model estimation.

• 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.

• 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.

• Added an option for defining legend labels and colours manually in plot.hmm.

• Fixed a bug when calling plot.mhmm inside a function. Thanks to Ellen Graham for catching the issue.

• Fixed an OpenMP sharing issue due to upcoming GCC9.

• 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.

• 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.

• 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.

• Fixed encoding issues in references.
• Updated author affiliations.

• 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.

• 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).

• 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.

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.

• 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.

As requested by CRAN, changed donttest example of interactive plotting to conditional block depending on whether session is interactive or not.

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.

First version on CRAN.

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