| acf_plot_dynamic | Create ACF plots from dynamic and ODBA data |
| acf_plot_log_odba | Create ACF plots from log ODBA data |
| acf_plot_static | Create ACF plots from static data |
| ar_bootstrap_ci | Confidence intervals for estimated parameters by... |
| ar_bootstrap_estimates | Get bootstrapped estimates of parameters |
| ar_densities | Returns densities for autoregressive model |
| ar_densities_labelled | Returns densities for autoregressive model, for some states... |
| ar_hmm_generate_sample | Generate sample from HMM with autoregressive model |
| ar_hmm_lbackward | Get backward probabilities |
| ar_hmm_lforward | Get forward probabilities |
| ar_hmm_mle | Maximum likelihood estimation of univariate autoregresive... |
| ar_hmm_mllk | Get negative log-likelihood from the working parameters |
| ar_hmm_pn2pw | Transform normal natural parameters to working parameters |
| ar_hmm_pseudo_residuals | Generate pseudo residuals |
| ar_hmm_pw2pn | Transform normal working parameters to natural parameters |
| ar_hmm_viterbi | Global decoding of states |
| ar_inv_hessian | Get inverse of hessian matrix |
| ar_jacobian | Get Jacobian matrix |
| behavior_hist_dynamic | Create histograms from dynamic and ODBA data, for each... |
| behavior_hist_log_odba | Create histograms from log ODBA data, for each behavior... |
| behavior_hist_static | Create histograms from static data, for each behavior... |
| behavior_pairs_plot_dynamic | Create correlation plots of X_dynamic, Y_dynamic, and... |
| behavior_pairs_plot_static | Create correlation plots of X_static, Y_static, and Z_static,... |
| behavior_plot_dynamic | Create line plots from dynamic and ODBA data, which are... |
| behavior_plot_log_odba | Create line plots from log ODBA data, which are colored by... |
| behavior_plot_static | Create line plots from static data, which are colored by... |
| diag_exp | Exponentiate diagonal elements |
| diag_log_lower | Get log diagonal and lower triangular entries |
| filtered_hist_dynamic | Create histograms from dynamic and ODBA data, aggregated by... |
| filtered_hist_log_odba | Create histograms from log ODBA data, aggregated by behavior |
| filtered_hist_static | Create histograms from static data, aggregated by behavior |
| get_all_ar_means | Get all means for autoregressive series |
| get_all_inmar_means | Get all means for multivariate autoregressive series |
| get_all_log_sd_data | Create multiple files containing dynamic and static log... |
| get_all_mar_means | Get all means for multivariate autoregressive series |
| get_all_mean_data | Create multiple files containing dynamic and static mean data |
| get_all_sd_data | Create multiple files containing dynamic and static standard... |
| get_ar_mean | Get mean corresponding to a given index in an autoregressive... |
| get_custom_data | Combine dynamic or static data with behavior timestamps |
| get_dynamic_log_sd_data | Get file of log standard deviations of dynamic data |
| get_dynamic_log_sd_plots | Create multiple plots for dynamic log standard deviation data |
| get_dynamic_mean_data | Get file of means of dynamic data |
| get_dynamic_mean_plots | Create multiple plots for dynamic mean data |
| get_dynamic_sd_data | Get file of standard deviations of dynamic data |
| get_dynamic_sd_plots | Create multiple plots for dynamic standard deviation data |
| get_inmar_mean | Get mean corresponding to a given index in an independent... |
| get_log_odba_mean_plots | Create multiple plots for log ODBA mean data |
| get_mar_mean | Get mean corresponding to a given index in a multivariate... |
| get_plots_dynamic | Create multiple plots for dynamic and ODBA data |
| get_plots_log_odba | Create multiple plots for log ODBA data |
| get_plots_static | Create multiple plots for static data |
| get_static_log_sd_data | Get file of log standard deviations of static data |
| get_static_log_sd_plots | Create multiple plots for static log standard deviation data |
| get_static_mean_data | Get file of means of static data |
| get_static_mean_plots | Create multiple plots for static mean data |
| get_static_sd_data | Get file of standard deviations of static data |
| get_static_sd_plots | Create multiple plots for static standard deviation data |
| graph_hmm_hist | Creates histogram from data generated from univariate HMM |
| graph_hmm_output | Creates a line plot from data generated from univariate HMM |
| hist_plot_dynamic | Create histograms from dynamic and ODBA data |
| hist_plot_log_odba | Create histogram from log ODBA data |
| hist_plot_static | Create histograms from static data |
| inmar_bootstrap_ci | Confidence intervals for estimated parameters by... |
| inmar_bootstrap_estimates | Get bootstrapped estimates of parameters |
| inmar_densities | Get matrix of state dependent probability densities |
| inmar_densities_labelled | Get matrix of state dependent probability densities, for some... |
| inmar_dist_mat | Get multivariate autoregressive distribution function |
| inmar_hmm_generate_sample | Generate samples from HMM with multivariate autoregressive... |
| inmar_hmm_lbackward | Get backward probabilities |
| inmar_hmm_lforward | Get forward probabilities |
| inmar_hmm_mle | Maximum likelihood estimation of multivariate normal... |
| inmar_hmm_mllk | Get negative log-likelihood from the working parameters |
| inmar_hmm_pn2pw | Transform multivariate autoregressive natural parameters to... |
| inmar_hmm_pseudo_residuals | Generate pseudo residuals |
| inmar_hmm_pw2pn | Transform multivariate autoregressive working parameters to... |
| inmar_hmm_viterbi | Global decoding of states |
| inmar_inv_hessian | Get inverse of hessian matrix |
| inmar_jacobian | Get Jacobian matrix |
| inmvnorm_bootstrap_ci | Confidence intervals for estimated parameters by... |
| inmvnorm_bootstrap_estimates | Get bootstrapped estimates of parameters |
| inmvnorm_densities | Get matrix of state dependent probability densities |
| inmvnorm_densities_labelled | Get matrix of state dependent probability densities |
| inmvnorm_dist_mat | Get multivariate normal distribution function |
| inmvnorm_hmm_generate_sample | Generate samples from HMM with independent multivariate... |
| inmvnorm_hmm_lbackward | Get backward probabilities |
| inmvnorm_hmm_lforward | Get forward probabilities |
| inmvnorm_hmm_mle | Maximum likelihood estimation of multivariate normal... |
| inmvnorm_hmm_mllk | Get negative log-likelihood from the working parameters |
| inmvnorm_hmm_pn2pw | Transform independent multivariate normal natural parameters... |
| inmvnorm_hmm_pseudo_residuals | Generate pseudo residuals |
| inmvnorm_hmm_pw2pn | Transform multivariate normal working parameters to natural... |
| inmvnorm_hmm_sample_one | Generate one sample from HMM with independent multivariate... |
| inmvnorm_hmm_viterbi | Global decoding of states |
| inmvnorm_inv_hessian | Get inverse of hessian matrix |
| inmvnorm_jacobian | Get Jacobian matrix |
| line_plot_dynamic | Create line plots from dynamic and ODBA data |
| line_plot_log_odba | Create line plots from log ODBA data |
| line_plot_static | Create line plots from static data |
| mar_bootstrap_ci | Confidence intervals for estimated parameters by... |
| mar_bootstrap_estimates | Get bootstrapped estimates of parameters |
| mar_densities | Get matrix of state dependent probability densities |
| mar_dist_mat | Get multivariate autoregressive distribution function |
| mar_hmm_generate_sample | Generate samples from HMM with multivariate autoregressive... |
| mar_hmm_lbackward | Get backward probabilities |
| mar_hmm_lforward | Get forward probabilities |
| mar_hmm_mle | Maximum likelihood estimation of multivariate normal... |
| mar_hmm_mllk | Get negative log-likelihood from the working parameters |
| mar_hmm_pn2pw | Transform multivariate autoregressive natural parameters to... |
| mar_hmm_pseudo_residuals | Generate pseudo residuals |
| mar_hmm_pw2pn | Transform multivariate autoregressive working parameters to... |
| mar_hmm_viterbi | Global decoding of states |
| mar_inv_hessian | Get inverse of hessian matrix |
| mar_jacobian | Get Jacobian matrix |
| mvnorm_bootstrap_ci | Confidence intervals for estimated parameters by... |
| mvnorm_bootstrap_estimates | Get bootstrapped estimates of parameters |
| mvnorm_densities | Get matrix of state dependent probability densities |
| mvnorm_dist_mat | Get multivariate normal distribution function |
| mvnorm_hmm_generate_sample | Generate samples from HMM with multivariate normal... |
| mvnorm_hmm_lbackward | Get backward probabilities |
| mvnorm_hmm_lforward | Get forward probabilities |
| mvnorm_hmm_mle | Maximum likelihood estimation of multivariate normal... |
| mvnorm_hmm_mllk | Get negative log-likelihood from the working parameters |
| mvnorm_hmm_pn2pw | Transform multivariate normal natural parameters to working... |
| mvnorm_hmm_pseudo_residuals | Generate pseudo residuals |
| mvnorm_hmm_pw2pn | Transform multivariate normal working parameters to natural... |
| mvnorm_hmm_sample_one | Generate one sample from HMM with multivariate normal... |
| mvnorm_hmm_viterbi | Global decoding of states |
| mvnorm_inv_hessian | Get inverse of hessian matrix |
| mvnorm_jacobian | Get Jacobian matrix |
| norm_bootstrap_ci | Confidence intervals for estimated parameters by... |
| norm_bootstrap_covariance | Estimate covariance matrix of parameters from bootstrap... |
| norm_bootstrap_estimates | Get bootstrapped estimates of parameters |
| norm_densities | Returns normal densities |
| norm_hmm_generate_sample | Generate sample from HMM with normal distribution |
| norm_hmm_lbackward | Get backward probabilities |
| norm_hmm_lforward | Get forward probabilities |
| norm_hmm_mle | Maximum likelihood estimation of univariate normal parameters |
| norm_hmm_mllk | Get negative log-likelihood from the working parameters |
| norm_hmm_pn2pw | Transform normal natural parameters to working parameters |
| norm_hmm_pseudo_residuals | Generate pseudo residuals |
| norm_hmm_pw2pn | Transform normal working parameters to natural parameters |
| norm_hmm_viterbi | Global decoding of states |
| norm_inv_hessian | Get inverse of hessian matrix |
| norm_jacobian | Get Jacobian matrix |
| norm_marginal | Get univariate normal marginal distribution from an HMM. |
| pacf_plot_dynamic | Create PACF plots from dynamic and ODBA data |
| pacf_plot_log_odba | Create PACF plots from log ODBA data |
| pacf_plot_static | Create PACF plots from static data |
| pairs_plot | Create correlation plot |
| pseudo_residual_plot | Pseudo residual plots |
| triangular_num | Get nth triangular number |
