seqHMM: Hidden Markov Models for Life Sequences and Other Multivariate, Multichannel Categorical Time Series

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Designed for fitting hidden (latent) Markov models and mixture hidden Markov models for social sequence data and other categorical time series. Also some more restricted versions of these type of models are available: Markov models, 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. The package provides functions for evaluating and comparing models, as well as functions for easy plotting of multichannel sequence data and hidden Markov models. Models are estimated using maximum likelihood via the EM algorithm and/or direct numerical maximization with analytical gradients. All main algorithms are written in C++ with support for parallel computation.

Author
Jouni Helske, Satu Helske
Date of publication
2016-08-01 17:29:47
Maintainer
Jouni Helske <jouni.helske@jyu.fi>
License
GPL (>= 2)
Version
1.0.6

View on CRAN

Man pages

biofam3c
Three-channel biofam data
build_hmm
Build a Hidden Markov Model
build_lcm
Build a Latent Class Model
build_mhmm
Build a Mixture Hidden Markov Model
build_mm
Build a Markov Model
build_mmm
Build a Mixture Markov Model
colorpalette
Color palettes
estimate_coef
Estimate Regression Coefficients of Mixture Hidden Markov...
fit_model
Estimate Parameters of (Mixture) Hidden Markov Models and...
forward_backward
Forward and Backward Probabilities for Hidden Markov Model
gridplot
Plot Multidimensional Sequence Plots in a Grid
hidden_paths
Most Probable Paths of Hidden States
hmm_biofam
Hidden Markov model for the biofam data
hmm_mvad
Hidden Markov model for the mvad data
logLik.hmm
Log-likelihood of the Hidden Markov Model
logLik.mhmm
Log-likelihood of the Mixture Hidden Markov Model
mc_to_sc
Transform a Multichannel Hidden Markov Model into a Single...
mc_to_sc_data
Merge Multiple Sequence Objects into One (from Multichannel...
mhmm_biofam
Mixture hidden Markov model for the biofam data
mhmm_mvad
Mixture hidden Markov model for the mvad data
mssplot
Interactive Stacked Plots of Multichannel Sequences and/or...
plot_colors
Plot Colorpalettes
plot.hmm
Plot hidden Markov models
plot.mhmm
Interactive Plotting for Mixed Hidden Markov Model (mhmm)
plot.ssp
Stack Multichannel Sequence Plots and/or Most Probable Paths...
posterior_probs
Posterior Probabilities for (Mixture) Hidden Markov Models
print
Print Method for a Hidden Markov Model
separate_mhmm
Reorganize a mixture hidden Markov model to a list of...
seqHMM
The seqHMM package
seqHMM-deprecated
Deprecated function(s) in the seqHMM package
simulate_hmm
Simulate hidden Markov models
simulate_mhmm
Simulate Mixture Hidden Markov Models
simulate_pars
Simulate Parameters of Hidden Markov Models
ssp
Define Arguments for Plotting Multichannel Sequences and/or...
ssplot
Stacked Plots of Multichannel Sequences and/or Most Probable...
summary.mhmm
Summary method for mixture hidden Markov models
TraMineR_imports
Imported Functions from 'TraMineR'
trim_model
Trim Small Probabilities of Hidden Markov Model
vcov.mhmm
Variance-Covariance Matrix for Coefficients of Covariates of...

Files in this package

seqHMM
seqHMM/inst
seqHMM/inst/doc
seqHMM/inst/doc/seqHMM.R
seqHMM/inst/doc/seqHMM.Rnw
seqHMM/inst/doc/seqHMM.pdf
seqHMM/src
seqHMM/src/viterbi.cpp
seqHMM/src/log_internalForward.cpp
seqHMM/src/forwardbackwardx.cpp
seqHMM/src/Makevars
seqHMM/src/EMx.cpp
seqHMM/src/log_EMx.cpp
seqHMM/src/EM.cpp
seqHMM/src/seqHMM.h
seqHMM/src/log_logLikMixHMM.cpp
seqHMM/src/uv_forwardbackward.cpp
seqHMM/src/log_logLikHMM.cpp
seqHMM/src/log_forwardbackwardx.cpp
seqHMM/src/viterbix.cpp
seqHMM/src/objective.cpp
seqHMM/src/objectivex.cpp
seqHMM/src/forwardbackward.cpp
seqHMM/src/log_internalBackward.cpp
seqHMM/src/internalForward.cpp
seqHMM/src/log_EM.cpp
seqHMM/src/logLikHMM.cpp
seqHMM/src/optCoef.cpp
seqHMM/src/logLikMixHMM.cpp
seqHMM/src/log_forwardbackward.cpp
seqHMM/src/internalBackward.cpp
seqHMM/src/varcoef.cpp
seqHMM/src/log_objectivex.cpp
seqHMM/src/RcppExports.cpp
seqHMM/src/log_objective.cpp
seqHMM/src/sa_opt_coef.cpp
seqHMM/src/logSumExp.cpp
seqHMM/src/log_optCoef.cpp
seqHMM/src/reparma.cpp
seqHMM/NAMESPACE
seqHMM/NEWS
seqHMM/data
seqHMM/data/biofam3c.rda
seqHMM/data/hmm_biofam.rda
seqHMM/data/mhmm_biofam.rda
seqHMM/data/colorpalette.rda
seqHMM/data/mhmm_mvad.rda
seqHMM/data/hmm_mvad.rda
seqHMM/R
seqHMM/R/plot_colors.R
seqHMM/R/mc_to_sc.R
seqHMM/R/simulate_pars.R
seqHMM/R/mHMMplotint.R
seqHMM/R/build_mmm.R
seqHMM/R/simulate_hmm.R
seqHMM/R/plot.mhmm.R
seqHMM/R/hmm_mvad.R
seqHMM/R/logLik.hmm.R
seqHMM/R/vcov.mhmm.R
seqHMM/R/hidden_paths.R
seqHMM/R/print.mhmm.R
seqHMM/R/forwardBackward.R
seqHMM/R/gridplot.R
seqHMM/R/separate_mhmm.R
seqHMM/R/import_seqdef.R
seqHMM/R/trim_hmm.R
seqHMM/R/posterior_probs.R
seqHMM/R/ssplotM.R
seqHMM/R/logLik.mhmm.R
seqHMM/R/colorpalette.R
seqHMM/R/spread_models.R
seqHMM/R/plot.igraph2.R
seqHMM/R/mhmm_mvad.R
seqHMM/R/mssplot.R
seqHMM/R/RcppExports.R
seqHMM/R/build_mm.R
seqHMM/R/plot.ssp.R
seqHMM/R/print.summary.mhmm.R
seqHMM/R/print.hmm.R
seqHMM/R/build_lcm.R
seqHMM/R/fit_model.R
seqHMM/R/build_mhmm.R
seqHMM/R/biofam3c.R
seqHMM/R/mHMMplotgrid.R
seqHMM/R/combine_models.R
seqHMM/R/ssplot.R
seqHMM/R/mhmm_biofam.R
seqHMM/R/seqHMM-deprecated.R
seqHMM/R/SSPlotter.R
seqHMM/R/ssp.R
seqHMM/R/help_data.R
seqHMM/R/isColor.R
seqHMM/R/simulate_mhmm.R
seqHMM/R/hmm_biofam.R
seqHMM/R/build_hmm.R
seqHMM/R/plot.hmm.R
seqHMM/R/seqHMM-package.R
seqHMM/R/summary.mhmm.R
seqHMM/R/HMMplot.R
seqHMM/R/estimate_coef.R
seqHMM/R/mc_to_sc_data.R
seqHMM/vignettes
seqHMM/vignettes/seqHMM.Rnw
seqHMM/vignettes/references.bib
seqHMM/MD5
seqHMM/build
seqHMM/build/vignette.rds
seqHMM/DESCRIPTION
seqHMM/man
seqHMM/man/mc_to_sc.Rd
seqHMM/man/mssplot.Rd
seqHMM/man/ssplot.Rd
seqHMM/man/build_mmm.Rd
seqHMM/man/biofam3c.Rd
seqHMM/man/mc_to_sc_data.Rd
seqHMM/man/seqHMM-deprecated.Rd
seqHMM/man/mhmm_mvad.Rd
seqHMM/man/simulate_hmm.Rd
seqHMM/man/plot_colors.Rd
seqHMM/man/plot.ssp.Rd
seqHMM/man/simulate_pars.Rd
seqHMM/man/trim_model.Rd
seqHMM/man/mhmm_biofam.Rd
seqHMM/man/estimate_coef.Rd
seqHMM/man/plot.mhmm.Rd
seqHMM/man/hmm_biofam.Rd
seqHMM/man/build_mhmm.Rd
seqHMM/man/TraMineR_imports.Rd
seqHMM/man/forward_backward.Rd
seqHMM/man/logLik.hmm.Rd
seqHMM/man/colorpalette.Rd
seqHMM/man/gridplot.Rd
seqHMM/man/build_lcm.Rd
seqHMM/man/fit_model.Rd
seqHMM/man/simulate_mhmm.Rd
seqHMM/man/separate_mhmm.Rd
seqHMM/man/summary.mhmm.Rd
seqHMM/man/build_mm.Rd
seqHMM/man/logLik.mhmm.Rd
seqHMM/man/hmm_mvad.Rd
seqHMM/man/ssp.Rd
seqHMM/man/seqHMM.Rd
seqHMM/man/build_hmm.Rd
seqHMM/man/hidden_paths.Rd
seqHMM/man/print.Rd
seqHMM/man/plot.hmm.Rd
seqHMM/man/posterior_probs.Rd
seqHMM/man/vcov.mhmm.Rd