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
NeedsCompilation: yes
Packaged: 2026-03-16 06:21:25 UTC; jvhels
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>
Repository: CRAN
Date/Publication: 2026-03-16 08:30:02 UTC
Built: R 4.6.1; x86_64-w64-mingw32; 2026-08-01 04:37:43 UTC; windows
Archs: x64
