Package: seqHMM
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
        Multivariate, Multichannel Categorical Time Series
Version: 2.2.0
Authors@R: 
    c(person(given = "Jouni",
           family = "Helske",
           role = c("aut", "cre"),
           email = "jouni.helske@iki.fi",
           comment = c(ORCID = "0000-0001-7130-793X")),
      person(given = "Satu",
           family = "Helske",
           role = "aut",
           comment = c(ORCID = "0000-0003-0532-0153")))
Description: Designed for estimating variants of hidden (latent) Markov
        models (HMMs), mixture HMMs, and non-homogeneous HMMs (NHMMs)
        for social sequence data and other categorical time series.
        Special cases include feedback-augmented NHMMs, Markov models
        without latent layer, mixture Markov models, and latent class
        models. The package supports models for one or multiple
        subjects with one or multiple parallel sequences (channels).
        External covariates can be added to explain cluster membership
        in mixture models as well as initial, transition and emission
        probabilities in NHMMs. The package provides functions for
        evaluating and comparing models, as well as functions for
        visualizing of multichannel sequence data and HMMs. For NHMMs,
        methods for computing average causal effects and marginal state
        and emission probabilities are available. Models are estimated
        using maximum likelihood via the EM algorithm or direct
        numerical maximization with analytical gradients. Documentation
        is available via several vignettes, and Helske and Helske
        (2019, <doi:10.18637/jss.v088.i03>). For methodology behind the
        NHMMs, see Helske (2025, <doi:10.48550/arXiv.2503.16014>).
LazyData: true
LinkingTo: nloptr, Rcpp (>= 0.12.0), RcppArmadillo
Depends: R (>= 4.1.0)
Imports: checkmate, cli, collapse, data.table (>= 1.16.0),
        future.apply, ggplot2, ggseqplot, graphics, grDevices, grid,
        gridBase, igraph, lhs, Matrix, methods, nloptr, numDeriv,
        patchwork, progressr, Rcpp (>= 0.12.0), RcppHungarian, rlang,
        stats, TraMineR (>= 2.2-7), utils
Suggests: covr, knitr, MASS, nnet, testthat (>= 3.0.0),
License: GPL (>= 2)
Encoding: UTF-8
BugReports: https://github.com/helske/seqHMM/issues
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Config/testthat/edition: 3
SystemRequirements: GNU make
Biarch: true
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libjpeg-dev
        libpng-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://helske.r-universe.dev
Date/Publication: 2026-03-15 14:14:16 UTC
RemoteUrl: https://github.com/helske/seqHMM
RemoteRef: HEAD
RemoteSha: f81ca78806730a84622af7c299eb745798c8c310
NeedsCompilation: yes
Packaged: 2026-06-13 08:06:15 UTC; root
Author: Jouni Helske [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7130-793X>),
  Satu Helske [aut] (ORCID: <https://orcid.org/0000-0003-0532-0153>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>