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

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.

AuthorJouni Helske, Satu Helske
Date of publication2016-08-01 17:29:47
MaintainerJouni Helske <jouni.helske@jyu.fi>
LicenseGPL (>= 2)
Version1.0.6

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...

Functions

alphabet Man page
biofam3c Man page
build_hmm Man page
build_lcm Man page
build_mhmm Man page
build_mm Man page
build_mmm Man page
colorpalette Man page
estimate_coef Man page
fit_hmm Man page
fit_mhmm Man page
fit_model Man page
forward_backward Man page
gridplot Man page
hidden_paths Man page
hmm_biofam Man page
hmm_mvad Man page
logLik.hmm Man page
logLik.mhmm Man page
mc_to_sc Man page
mc_to_sc_data Man page
mhmm_biofam Man page
mhmm_mvad Man page
mssplot Man page
plot_colors Man page
plot.hmm Man page
plot.mhmm Man page
plot.ssp Man page
posterior_probs Man page
print.hmm Man page
print.mhmm Man page
print.summary.mhmm Man page
separate_mhmm Man page
seqdef Man page
seqHMM Man page
seqHMM-deprecated Man page
seqHMM-deprecated-package Man page
seqHMM-package Man page
seqstatf Man page
simulate_emission_probs Man page
simulate_hmm Man page
simulate_initial_probs Man page
simulate_mhmm Man page
simulate_transition_probs Man page
ssp Man page
ssplot Man page
summary.mhmm Man page
trim_hmm Man page
trim_model Man page
vcov.mhmm Man page

Files

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

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