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| apply_viterbi | Viterbi algorithm |
| check_controls | Controls check |
| check_decoding | Decoding check |
| check_estimation | Estimation check |
| check_saving | Saving check |
| compute_ci | Confidence intervals |
| compute_fs | Fine-scale chunk lengths |
| create_visuals | Visualization |
| dfCon2dfUncon | Unconstrains degrees of freedom. |
| dfUncon2dfCon | Constrains degrees of freedom. |
| download_data | Data download |
| exception | Debugging |
| fit_hmm | Fit (hierarchical) hidden Markov models to financial data |
| Gamma2delta | Computes stationary distribution of transition probability matrix. |
| Gamma2gammasCon | Constrains non-diagonal matrix elements of transition probability matrix. |
| Gamma2gammasUncon | Unconstraines non-diagonal matrix elements of transition probability matrix. |
| gammasCon2Gamma | Builds transition probability matrix from constrained non-diagonal elements. |
| gammasCon2gammasUncon | Unconstrains non-diagonal elements of transition probability matrix. |
| gammasUncon2Gamma | Builds transition probability matrix from unconstrained non-diagonal elements. |
| gammasUncon2gammasCon | Constrains non-diagonal elements of transition probability matrix. |
| init_est | Initialisation |
| max_likelihood | Optimization |
| muCon2muUncon | Unconstrains expected values. |
| muUncon2muCon | Constrains expected values. |
| nLL_hhmm | Negative log-likelihood of a HHMM |
| nLL_hmm | Negative log-likelihood of a HMM |
| parameter_names | Parameter names |
| plot_ll | Visualization of log-likelihood values |
| plot_sdd | Visualization of estimated state-dependent distributions |
| plot_ts | Visualize decoded time-series |
| process_data | Data processing |
| pseudo_residuals | Pseudo-residuals |
| read_data | Read .csv-file |
| sigmaCon2sigmaUncon | Unconstrains standard deviations. |
| sigmaUncon2sigmaCon | Constrains standard deviations. |
| simulate_data | Data simulation |
| thetaCon2thetaList | Brings contrained model parameters from vector form 'thetaCon' to list form 'ThetaList'. |
| thetaCon2thetaUncon | Unconstrains model parameters. |
| thetaList2thetaCon | Brings constrained model parameters from list form 'thetaList' to vector form 'thetaCon'. |
| thetaList2thetaListOrdered | Orders states in 'thetaList' based on expected values. |
| thetaList2thetaUncon | Brings constrained model parameters in list form to unconstrained parameters in vector form. |
| thetaUncon2thetaCon | Constrains model parameters. |
| thetaUncon2thetaList | Brings uncontrained model parameters 'thetaUncon' in list form 'thetaList'. |
| thetaUncon2thetaUnconSplit | Splits uncontrained model parameters 'thetaUncon' by fine-scale HMMs. |
| thetaUnconSplit2thetaList | Brings uncontrained fine-scale model parameters in constrained list form. |