%sp%                    Sparsity-retaining matrix multiplication
LaMaColors              Generate a colour-blind-friendly palette
MCreport                Sample parameters from approximate Gaussian
                        posterior distribution
calc_trackInd           Calculate the index of the first observation of
                        each track based on an ID variable
cosinor                 Trigonometric basis expansion
ddwell                  State dwell-time distributions of periodically
                        inhomogeneous Markov chains
dgmrf2                  Reparametrised multivariate Gaussian
                        distribution
forward                 Forward algorithm to calculate the HMM
                        log-likelihood
forward_g               Forward algorithm with time-varying transition
                        probability matrix
forward_hsmm            Forward algorithm for homogeneous hidden
                        semi-Markov models
forward_ihsmm           Forward algorithm for hidden semi-Markov models
                        with inhomogeneous state durations and/ or
                        conditional transition probabilities
forward_p               Forward algorithm with for periodically varying
                        transition probability matrices
forward_phsmm           Forward algorithm for hidden semi-Markov models
                        with periodically inhomogeneous state durations
                        and/ or conditional transition probabilities
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
gamma2                  Reparametrised gamma distribution
gdeterminant            Computes generalised determinant
generator               Build the generator matrix of a continuous-time
                        Markov chain
generator_g             Build generator matrices of a continuous-time
                        Markov chain
logLik.LaMaModel        Extract log-likelihood from LaMaModel object
logLik.qremlModel       Extract log-likelihood from qremlModel object
make_matrices           Build the design and the penalty matrix for
                        models involving penalised splines based on a
                        formula and a data set
make_matrices_dens      Build a standardised P-Spline design matrix and
                        the associated P-Spline penalty matrix
make_matrices_old       Build the design and the penalty matrix for
                        models involving penalised splines based on a
                        formula and a data set
minmax                  AD-compatible minimum and maximum functions
minmax0_smooth          Smooth approximations to max(x, 0) and min(x,
                        0)
nessi                   Loch Ness Monster Acceleration Data
penalty                 Computes penalty based on quadratic form
penalty2                Computes generalised quadratic-form penalties
penalty_uni             Penalty approximation of unimodality
                        constraints for univariates smooths
plot.LaMaResiduals      Plot pseudo-residuals
pred_matrix             Build the prediction design matrix based on new
                        data and model_matrices object created by
                        'make_matrices'
predict.LaMa_matrices   Build the prediction design matrix based on new
                        data and model_matrices object created by
                        'make_matrices'
process_hid_formulas    Process and standardise formulas for the state
                        process of hidden Markov models
pseudo_res              Calculate pseudo-residuals
qreml                   Quasi restricted maximum likelihood (qREML)
                        algorithm for models with penalised splines or
                        simple i.i.d. random effects
qreml_old               Quasi restricted maximum likelihood (qREML)
                        algorithm for models with penalised splines or
                        simple i.i.d. random effects
report                  Get reported quantities from and 'RTMB' object
                        and return a 'LaMaModel'
sdreportMC              Monte Carlo version of 'sdreport'
sdreport_outer          Report uncertainty of the estimated smoothing
                        parameters or variances
skewnorm                Skew normal distribution
smooth_dens_construct   Build the design and penalty matrices for
                        smooth density estimation
stateprobs              Calculate conditional local state probabilities
                        in 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_ct           Compute the stationary distribution of a
                        continuous-time Markov chain
stationary_p            Periodically stationary distribution of a
                        periodically inhomogeneous Markov chain
stationary_p_sparse     Sparse version of 'stationary_p'
stationary_sparse       Sparse version of 'stationary'
summary.qremlModel      Summary method for 'qremlModel' objects
tpm                     Build the transition probability matrix from
                        unconstrained parameter vector
tpm_ct                  Calculate continuous time transition
                        probabilities
tpm_emb                 Build the embedded transition probability
                        matrix of an HSMM from unconstrained parameter
                        vector
tpm_emb_g               Build all embedded transition probability
                        matrices of an inhomogeneous HSMM
tpm_g                   Build all transition probability matrices of an
                        inhomogeneous HMM
tpm_g2                  Build all transition probability matrices of an
                        inhomogeneous HMM
tpm_hsmm                Builds the transition probability matrix of an
                        HSMM-approximating HMM
tpm_hsmm2               Build the transition probability matrix of an
                        HSMM-approximating HMM
tpm_ihsmm               Builds all transition probability matrices of
                        an inhomogeneous-HSMM-approximating HMM
tpm_p                   Build all transition probability matrices of a
                        periodically inhomogeneous HMM
tpm_phsmm               Builds all transition probability matrices of
                        an periodic-HSMM-approximating HMM
tpm_phsmm2              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.
trex                    T-Rex Movement Data
trigBasisExp            Compute the design matrix for a trigonometric
                        basis expansion
viterbi                 Viterbi algorithm for state decoding in HMMs
viterbi_g               Viterbi algorithm for state decoding in
                        inhomogeneous HMMs
viterbi_p               Viterbi algorithm for state decoding in
                        periodically inhomogeneous HMMs
vm                      Von Mises distribution
wrpcauchy               Wrapped Cauchy distribution
zero_inflate            Zero-inflated density constructer
