# Fast Numerical Maximum Likelihood Estimation for Latent Markov Models

## Documentation for package ‘LaMa’ version 1.0.0

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

## Help Pages

calc_trackInd | Calculate the index of the first observation of each track based on an ID variable
forward | Forward algorithm with homogeneous transition probability matrix
forward_g | General forward algorithm with time-varying transition probability matrix
forward_p | Forward algorithm with (only) periodically varying transition probability matrix
forward_s | Forward algorithm for hidden semi-Markov models with homogeneous transition probability matrix
forward_sp | Forward algorithm for hidden semi-Markov models with periodically varying transition probability matrices
stateprobs | Calculate conditional local state probabilities for homogeneous HMMs
stateprobs_g | Calculate conditional local state probabilities for inhomogeneous HMMs
stateprobs_p | Calculate conditional local state probabilities for periodically inhomogeneous HMMs
stationary | Compute the stationary distribution of a homogeneous Markov chain
stationary_p | Compute the periodically stationary distribution of a periodically inhomogeneous Markov chain
tpm | Build the transition probability matrix from unconstraint parameter vector
tpm_cont | Calculation of continuous time transition probabilities
tpm_g | Build all transition probability matrices of an inhomogeneous HMM
tpm_hsmm | Build the transition probability matrix of an HSMM-approximating HMM
tpm_p | Build all transition probability matrices of a periodically inhomogeneous HMM
tpm_phsmm | Build all transition probability matrices of an periodic-HSMM-approximating HMM
tpm_thinned | Compute the transition probability matrix of a thinned periodically inhomogeneous Markov chain.
trigBasisExp | Trigonometric Basis Expansion
viterbi | Viterbi algorithm for decoding states
viterbi_g | Viterbi algorithm for decoding states of inhomogeneous HMMs
viterbi_p | Viterbi algorithm for decoding states of periodically inhomogeneous HMMs