| append_missing | Append missing objects to the irm arrays and eigen... |
| BDAepimodel-package | Fit Stochastic Epidemic Models in R via Bayesian Data... |
| buildEigenArray | Update eigen values, vectors, and inverse matrices for irms |
| buildEigenArray_SEIR | Update eigen values, vectors, and inverse matrices... |
| buildEigenArray_SIR | Update eigen values, vectors, and inverse matrices... |
| build_emission_mat | Updates the matrix of emission probabilities |
| buildFBMats | Construct forward-backward matrices |
| build_initdist | Construct the vector with initial state probabilities for a... |
| build_irm | Construct an environment of rate matrices and another... |
| build_new_irms | Build a new array of rate matrices |
| buildRateArray | Update an array of rate matrices with the current rates |
| build_rate_mat | Construct a single rate matrix from a vector of rates and a... |
| build_tpm | Construct a transition probability matrix from |
| build_tpm_seqs | Construct the sequences of transition probability matrix... |
| calc_obs_likelihood | Calculate likelihood for the population level trajectory and... |
| calc_pop_likelihood | Calculate likelihood for the population level trajectory |
| check_irm | Checks that all of the IRMs that are required exist in the... |
| complexTPM | Construct a transition probability matrix for a rate matrix... |
| detect_structure | Detects whether there is structure in the stochastic epidemic... |
| draw_trajec | Sample a subject-level trajectory. |
| est_scale_template | Template for function for transformint to the estimation... |
| expand_pop_mat | Add buffer rows to a pop_mat matrix to enable in-place... |
| expit | expit function |
| extract_rate_fcns | Extracts a list of functions for computing flow rates. |
| fit_epimodel | Main wrapper to fit a stochastic epimodel using the Bayesian... |
| generate_keys | Generate the keys for indexing into the .irm and .eigen... |
| getObsTimeInds | Get the indices of observation times in the population level... |
| get_tpms_to_build | Get the indices for the transition probability matrices to be... |
| gibbs_template | Template for Gibbs kernel |
| hello | Hello, World! |
| init_augmentation | Generate an initial configuration that is concordant with the... |
| init_config_mat | initializes the bookkeeping object for population level... |
| init_epimodel | Initialize epimodel bookkeeping object. |
| init_irm | Initialize an arrays for storing matrices of rates,... |
| init_obs_mat | Initializes a bookkeeping object for the observed and... |
| init_rate_map | Construct an index matrix identifying with which states each... |
| init_results | Initialize list for storing results |
| init_settings | Initialize a bookkeeping list of MCMC settings. |
| init_state_lookup | Insert a lookup table to map subjects at risk for each... |
| init_trajectories | Initialize a set of trajectories if an initial set of paths... |
| init_tuning | Initialize tuning for M-H kernels. |
| insertPath | Insert subject transitions into the population-level and... |
| insert_row | Generic function to insert a row into a matrix. |
| insert_trajectory | Insert a newly sampled subject-level trajectory so its... |
| irm_decomp | Compute the eigen decomposition for a rate matrix, and either... |
| joinCubes | Join two armadillo cubes |
| logit | logit function |
| match_row | Returns either a logical vector of indices for which row(s)... |
| MH_accept_reject | Accept or reject a proposed subject-level trajectory via MH... |
| mh_template | Template for Metropolis-Hastings kernel |
| normalize | Normalize a vector or matrix. |
| plot_epimodel | Plot the current trajectory and data in an epimodel object... |
| plot_latent_posterior | Plot the posterior distribution of the latent paths for... |
| populationLikelihood | Get the irm keys for the compartment counts in a population... |
| prepare_epimodel | Prepares an epimodel environment. |
| rcpp_hello | Hello, Rcpp! |
| reinsert_path | Re-insert the current path back into the configuration... |
| remove_trajectory | Remove the contribution of a subject from the compartment... |
| reorderMat | Reorder the rows of a matrix |
| resolveSubjContrib | Add or remove the subject contribution from the compartment... |
| retrieveKeys | Get the irm keys for the compartment counts in a population... |
| retrieveSubjPath | Insert subject transitions into the population-level and... |
| sample_at_event_times | Sample the infection status at times of state transition of... |
| sample_at_obs_times | Sample the infection status for the specified subject at... |
| sampleEventSubseq | Update eigen values, vectors, and inverse matrices for irms |
| sample_forward | Forward path sampling. |
| sample_path | Wrapper for sampling the path within homogeneous intervals. |
| sim_one_event | Simulate the next event using Gillespie's next reaction... |
| simulateSIR | simulateSIR function, included in this file because of... |
| simulate_SIR | Simulate an epidemic with SIR dynamics and draw binomial... |
| subjectLikelihood | Get the irm keys for the compartment counts in a population... |
| subject_probabilities | Build a vector of probabilities according to which subjects... |
| templates | Generates a template script for specifying a transition... |
| tpmProdSeqs | Update eigen values, vectors, and inverse matrices for irms |
| tpmSeqs | Update eigen values, vectors, and inverse matrices for irms |
| traj_to_obs | Instatiates a data matrix based on a configuration matrix.... |
| tune_proposal | Tune proposal distribution for randow walk M-H parameter... |
| update_obs_mat | Update the observation matrix and the indices of observation... |
| update_params | Replace the vector of parameters in an epimodel object with... |
| update_tpms | Update the list of tpms and tpm products to reflect the... |
