seqHMM: Hidden Markov Models for Life Sequences and Other Multivariate, Multichannel Categorical Time Series
Version 1.0.7

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.

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AuthorJouni Helske, Satu Helske
Date of publication2017-04-04 17:17:35 UTC
MaintainerJouni Helske <jouni.helske@jyu.fi>
LicenseGPL (>= 2)
Version1.0.7
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("seqHMM")

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

EM Source code
EMx Source code
HMMplot Source code
SSPlotter Source code
alphabet Man page
biofam3c Man page
build_hmm Man page Source code
build_lcm Man page Source code
build_mhmm Man page Source code
build_mm Man page Source code
build_mmm Man page Source code
colorpalette Man page
combine_models Source code
estimate_coef Man page Source code
estimate_coefs Source code
fit_hmm Man page Source code
fit_mhmm Man page Source code
fit_model Man page Source code
forward_backward Man page Source code
forwardbackward Source code
forwardbackwardx Source code
gridplot Man page Source code
hidden_paths Man page Source code
hmm_biofam Man page
hmm_mvad Man page
isColor Source code
logLik.hmm Man page Source code
logLik.mhmm Man page Source code
logLikHMM Source code
logLikMixHMM Source code
logSumExp Source code
log_EM Source code
log_EMx Source code
log_forwardbackward Source code
log_forwardbackwardx Source code
log_logLikHMM Source code
log_logLikMixHMM Source code
log_objective Source code
log_objectivex Source code
mHMMplotgrid Source code
mHMMplotint Source code
mc_to_sc Man page Source code
mc_to_sc_data Man page Source code
mhmm_biofam Man page
mhmm_mvad Man page
mssplot Man page Source code
objective Source code
objectivex Source code
plot.hmm Man page Source code
plot.igraph2 Source code
plot.mhmm Man page Source code
plot.ssp Man page Source code
plot_colors Man page Source code
posterior_probs Man page Source code
print.hmm Man page Source code
print.mhmm Man page Source code
print.summary.mhmm Man page Source code
separate_mhmm Man page Source code
seqHMM Man page
seqHMM-deprecated Man page
seqHMM-deprecated-package Man page
seqHMM-package Man page
seqdef Man page
seqstatf Man page
simulate_emission_probs Man page Source code
simulate_hmm Man page Source code
simulate_initial_probs Man page Source code
simulate_mhmm Man page Source code
simulate_transition_probs Man page Source code
spread_models Source code
ssp Man page Source code
ssplot Man page Source code
ssplotM Source code
summary.mhmm Man page Source code
trim_hmm Man page Source code
trim_model Man page Source code
varcoef Source code
vcov.mhmm Man page Source code
viterbi Source code
viterbix Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/seqHMM.R
inst/doc/seqHMM_algorithms.Rnw
inst/doc/seqHMM.Rnw
inst/doc/seqHMM_algorithms.pdf
inst/doc/seqHMM_visualization.Rnw
inst/doc/seqHMM_estimation.Rnw
inst/doc/seqHMM_visualization.pdf
inst/doc/seqHMM_estimation.pdf
inst/doc/seqHMM.pdf
inst/doc/seqHMM_visualization.R
src
src/viterbi.cpp
src/log_internalForward.cpp
src/forwardbackwardx.cpp
src/Makevars
src/EMx.cpp
src/log_EMx.cpp
src/EM.cpp
src/seqHMM.h
src/log_logLikMixHMM.cpp
src/uv_forwardbackward.cpp
src/log_logLikHMM.cpp
src/log_forwardbackwardx.cpp
src/viterbix.cpp
src/objective.cpp
src/objectivex.cpp
src/forwardbackward.cpp
src/log_internalBackward.cpp
src/internalForward.cpp
src/log_EM.cpp
src/logLikHMM.cpp
src/optCoef.cpp
src/logLikMixHMM.cpp
src/log_forwardbackward.cpp
src/internalBackward.cpp
src/varcoef.cpp
src/log_objectivex.cpp
src/init.c
src/RcppExports.cpp
src/log_objective.cpp
src/sa_opt_coef.cpp
src/logSumExp.cpp
src/log_optCoef.cpp
src/reparma.cpp
NAMESPACE
NEWS
data
data/biofam3c.rda
data/hmm_biofam.rda
data/mhmm_biofam.rda
data/colorpalette.rda
data/mhmm_mvad.rda
data/hmm_mvad.rda
R
R/plot_colors.R
R/mc_to_sc.R
R/simulate_pars.R
R/mHMMplotint.R
R/build_mmm.R
R/simulate_hmm.R
R/plot.mhmm.R
R/hmm_mvad.R
R/logLik.hmm.R
R/vcov.mhmm.R
R/hidden_paths.R
R/print.mhmm.R
R/forwardBackward.R
R/gridplot.R
R/separate_mhmm.R
R/import_seqdef.R
R/trim_hmm.R
R/posterior_probs.R
R/ssplotM.R
R/logLik.mhmm.R
R/colorpalette.R
R/spread_models.R
R/plot.igraph2.R
R/mhmm_mvad.R
R/mssplot.R
R/RcppExports.R
R/build_mm.R
R/plot.ssp.R
R/print.summary.mhmm.R
R/print.hmm.R
R/build_lcm.R
R/fit_model.R
R/build_mhmm.R
R/biofam3c.R
R/mHMMplotgrid.R
R/combine_models.R
R/ssplot.R
R/mhmm_biofam.R
R/seqHMM-deprecated.R
R/SSPlotter.R
R/ssp.R
R/help_data.R
R/isColor.R
R/simulate_mhmm.R
R/hmm_biofam.R
R/build_hmm.R
R/plot.hmm.R
R/seqHMM-package.R
R/summary.mhmm.R
R/HMMplot.R
R/estimate_coef.R
R/mc_to_sc_data.R
vignettes
vignettes/seqHMM_algorithms.Rnw
vignettes/seqHMM.Rnw
vignettes/references_for_vignettes.bib
vignettes/seqHMM_visualization.Rnw
vignettes/seqHMM_estimation.Rnw
vignettes/seqHMM-concordance.tex
vignettes/seqHMM_algorithms-concordance.tex
vignettes/references.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/mc_to_sc.Rd
man/mssplot.Rd
man/ssplot.Rd
man/build_mmm.Rd
man/biofam3c.Rd
man/mc_to_sc_data.Rd
man/seqHMM-deprecated.Rd
man/mhmm_mvad.Rd
man/simulate_hmm.Rd
man/plot_colors.Rd
man/plot.ssp.Rd
man/simulate_pars.Rd
man/trim_model.Rd
man/mhmm_biofam.Rd
man/estimate_coef.Rd
man/plot.mhmm.Rd
man/hmm_biofam.Rd
man/build_mhmm.Rd
man/TraMineR_imports.Rd
man/forward_backward.Rd
man/logLik.hmm.Rd
man/colorpalette.Rd
man/gridplot.Rd
man/build_lcm.Rd
man/fit_model.Rd
man/simulate_mhmm.Rd
man/separate_mhmm.Rd
man/summary.mhmm.Rd
man/build_mm.Rd
man/logLik.mhmm.Rd
man/hmm_mvad.Rd
man/ssp.Rd
man/seqHMM.Rd
man/build_hmm.Rd
man/hidden_paths.Rd
man/print.Rd
man/plot.hmm.Rd
man/posterior_probs.Rd
man/vcov.mhmm.Rd
seqHMM documentation built on May 20, 2017, 5:46 a.m.