Fit Stochastic Epidemic Models in R via Bayesian Data Augmentation

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... |

simulate_epimodel | Simulates a stochastic epidemic model. |

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... |

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