# Mixture Hidden Markov Models for Social Sequence Data and Other Multivariate, Multichannel Categorical Time Series

## Documentation for package ‘seqHMM’ version 2.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

B C D E F G H L M N P R S T U V

seqHMM-package | The seqHMM package

## -- B --

biofam3c | Three-channel biofam data
bootstrap_coefs | Bootstrap Sampling of NHMM Coefficients
bootstrap_coefs.mnhmm | Bootstrap Sampling of NHMM Coefficients
bootstrap_coefs.nhmm | Bootstrap Sampling of NHMM Coefficients
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

## -- C --

cluster_names | Get Cluster Names from Mixture HMMs
cluster_names<- | Set Cluster Names for Mixture Models
coef.mnhmm | Get the Estimated Regression Coefficients of Non-Homogeneous Hidden Markov Models
coef.nhmm | Get the Estimated Regression Coefficients of Non-Homogeneous Hidden Markov Models
colorpalette | Color palettes

## -- D --

data_to_stslist | Transform TraMineR's state sequence object to data.table and vice versa

## -- E --

estimate_mnhmm | Estimate a Mixture Non-homogeneous Hidden Markov Model
estimate_nhmm | Estimate a Non-homogeneous Hidden Markov Model

## -- F --

fanhmm_leaves | A feedback-augmented non-homogeneous hidden Markov Model for leaves data
fit_model | Estimate Parameters of (Mixture) Hidden Markov Models and Their Restricted Variants
forward_backward | Forward and Backward Probabilities for Hidden Markov Model
forward_backward.hmm | Forward and Backward Probabilities for Hidden Markov Model
forward_backward.mhmm | Forward and Backward Probabilities for Hidden Markov Model
forward_backward.mnhmm | Forward and Backward Probabilities for Hidden Markov Model
forward_backward.nhmm | Forward and Backward Probabilities for Hidden Markov Model

## -- G --

get_cluster_probs | Extract the Prior Cluster Probabilities of MHMM or MNHMM
get_cluster_probs.mhmm | Extract the Prior Cluster Probabilities of MHMM or MNHMM
get_cluster_probs.mnhmm | Extract the Prior Cluster Probabilities of MHMM or MNHMM
get_emission_probs | Extract the Emission Probabilities of Hidden Markov Model
get_emission_probs.hmm | Extract the Emission Probabilities of Hidden Markov Model
get_emission_probs.mhmm | Extract the Emission Probabilities of Hidden Markov Model
get_emission_probs.mnhmm | Extract the Emission Probabilities of Hidden Markov Model
get_emission_probs.nhmm | Extract the Emission Probabilities of Hidden Markov Model
get_initial_probs | Extract the Initial State Probabilities of Hidden Markov Model
get_initial_probs.hmm | Extract the Initial State Probabilities of Hidden Markov Model
get_initial_probs.mhmm | Extract the Initial State Probabilities of Hidden Markov Model
get_initial_probs.mnhmm | Extract the Initial State Probabilities of Hidden Markov Model
get_initial_probs.nhmm | Extract the Initial State Probabilities of Hidden Markov Model
get_marginals | Compute the Marginal Probabilities from NHMMs
get_transition_probs | Extract the State Transition Probabilities of Hidden Markov Model
get_transition_probs.hmm | Extract the State Transition Probabilities of Hidden Markov Model
get_transition_probs.mhmm | Extract the State Transition Probabilities of Hidden Markov Model
get_transition_probs.mnhmm | Extract the State Transition Probabilities of Hidden Markov Model
get_transition_probs.nhmm | Extract the State Transition Probabilities of Hidden Markov Model
gridplot | Plot Multidimensional Sequence Plots in a Grid

## -- H --

hidden_paths | Most Probable Paths of Hidden States
hidden_paths.hmm | Most Probable Paths of Hidden States
hidden_paths.mhmm | Most Probable Paths of Hidden States
hidden_paths.mnhmm | Most Probable Paths of Hidden States
hidden_paths.nhmm | Most Probable Paths of Hidden States
hmm_biofam | Hidden Markov model for the biofam data
hmm_mvad | Hidden Markov model for the mvad data

## -- L --

leaves | Synthetic data on fathers' parental leaves in Finland
logLik.hmm | Log-likelihood of a Hidden Markov Model
logLik.mhmm | Log-likelihood of a Hidden Markov Model
logLik.mnhmm | Log-likelihood of a Non-homogeneous Hidden Markov Model
logLik.nhmm | Log-likelihood of a Non-homogeneous Hidden Markov Model

## -- M --

mc_to_sc | Transform a Multichannel Hidden Markov Model into a Single Channel Representation
mc_to_sc_data | Merge Multiple Sequence Objects into One (from Multichannel to Single Channel Data)
mhmm_biofam | Mixture hidden Markov model for the biofam data
mhmm_mvad | Mixture hidden Markov model for the mvad data
most_probable_cluster | Extract Most Probable Cluster for Each Sequence
mssplot | Interactive Stacked Plots of Multichannel Sequences and/or Most Probable Paths for Mixture Hidden Markov Models

## -- N --

nobs.hmm | Number of Observations in Hidden Markov Model
nobs.mhmm | Number of Observations in Hidden Markov Model
nobs.mnhmm | Number of Observations in Hidden Markov Model
nobs.nhmm | Number of Observations in Hidden Markov Model

## -- P --

permute_states | Permute the states of NHMM using Hungarian algorithm
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 Plots from Hidden Markov Models
plot_colors | Plot Colorpalettes
posterior_cluster_probabilities | Extract Posterior Cluster Probabilities
posterior_probs | Posterior Probabilities for Hidden Markov Models
posterior_probs.hmm | Posterior Probabilities for Hidden Markov Models
posterior_probs.mhmm | Posterior Probabilities for Hidden Markov Models
posterior_probs.mnhmm | Posterior Probabilities for Hidden Markov Models
posterior_probs.nhmm | Posterior Probabilities for Hidden Markov Models
predict.mnhmm | Predictions from Non-homogeneous Hidden Markov Models
predict.nhmm | Predictions from Non-homogeneous Hidden Markov Models
print.hmm | Print Method for a Hidden Markov Model
print.mhmm | Print Method for a Hidden Markov Model
print.mnhmm | Print Method for a Hidden Markov Model
print.nhmm | Print Method for a Hidden Markov Model
print.summary_mhmm | Print Method for a Hidden Markov Model

## -- R --

return_msg | Convert return code from estimate_nhmm and estimate_mnhmm to text

## -- S --

separate_mhmm | Reorganize a mixture hidden Markov model to a list of separate hidden Markov models (covariates ignored)
seqHMM | The seqHMM package
seqHMM-deprecated | Deprecated function(s) in the seqHMM package
simulate_emission_probs | Simulate Parameters of Hidden Markov Models
simulate_hmm | Simulate hidden Markov models
simulate_initial_probs | Simulate Parameters of Hidden Markov Models
simulate_mhmm | Simulate Mixture Hidden Markov Models
simulate_mnhmm | Simulate Mixture Non-homogeneous Hidden Markov Models
simulate_nhmm | Simulate Non-homogeneous Hidden Markov Models
simulate_transition_probs | Simulate Parameters of Hidden Markov Models
sort_sequences | Sort sequences in a sequence object
ssp | Define Arguments for Plotting Multichannel Sequences and/or Most Probable Paths from Hidden Markov Models
ssplot | Stacked Plots of Multichannel Sequences and/or Most Probable Paths from Hidden Markov Models
stacked_sequence_plot | Stacked Sequence Plots of Multichannel Sequences and/or Most Probable Paths from Hidden Markov Models
state_names | Get State Names of Hidden Markov Model
state_names.hmm | Get State Names of Hidden Markov Model
state_names.mhmm | Get State Names of Hidden Markov Model
state_names.mnhmm | Get State Names of Hidden Markov Model
state_names.nhmm | Get State Names of Hidden Markov Model
state_names<- | Get State Names of Hidden Markov Model
state_names<-.hmm | Get State Names of Hidden Markov Model
state_names<-.mhmm | Get State Names of Hidden Markov Model
state_names<-.mnhmm | Get State Names of Hidden Markov Model
state_names<-.nhmm | Get State Names of Hidden Markov Model
stslist_to_data | Transform TraMineR's state sequence object to data.table and vice versa
summary.mhmm | Summary method for mixture hidden Markov models
summary.mnhmm | Summary method for mixture non-homogenous hidden Markov models

## -- T --

trim_model | Trim Small Probabilities of Hidden Markov Model

## -- U --

update.mnhmm | Update Covariate Values of NHMM
update.nhmm | Update Covariate Values of NHMM

## -- V --

vcov.mhmm | Variance-Covariance Matrix for Coefficients of Covariates of Mixture Hidden Markov Model