Man pages for fintzij/BDAepimodel
Fit Stochastic Epidemic Models in R via Bayesian Data Augmentation

append_missingAppend missing objects to the irm arrays and eigen...
BDAepimodel-packageFit Stochastic Epidemic Models in R via Bayesian Data...
buildEigenArrayUpdate eigen values, vectors, and inverse matrices for irms
buildEigenArray_SEIRUpdate eigen values, vectors, and inverse matrices...
buildEigenArray_SIRUpdate eigen values, vectors, and inverse matrices...
build_emission_matUpdates the matrix of emission probabilities
buildFBMatsConstruct forward-backward matrices
build_initdistConstruct the vector with initial state probabilities for a...
build_irmConstruct an environment of rate matrices and another...
build_new_irmsBuild a new array of rate matrices
buildRateArrayUpdate an array of rate matrices with the current rates
build_rate_matConstruct a single rate matrix from a vector of rates and a...
build_tpmConstruct a transition probability matrix from
build_tpm_seqsConstruct the sequences of transition probability matrix...
calc_obs_likelihoodCalculate likelihood for the population level trajectory and...
calc_pop_likelihoodCalculate likelihood for the population level trajectory
check_irmChecks that all of the IRMs that are required exist in the...
complexTPMConstruct a transition probability matrix for a rate matrix...
detect_structureDetects whether there is structure in the stochastic epidemic...
draw_trajecSample a subject-level trajectory.
est_scale_templateTemplate for function for transformint to the estimation...
expand_pop_matAdd buffer rows to a pop_mat matrix to enable in-place...
expitexpit function
extract_rate_fcnsExtracts a list of functions for computing flow rates.
fit_epimodelMain wrapper to fit a stochastic epimodel using the Bayesian...
generate_keysGenerate the keys for indexing into the .irm and .eigen...
getObsTimeIndsGet the indices of observation times in the population level...
get_tpms_to_buildGet the indices for the transition probability matrices to be...
gibbs_templateTemplate for Gibbs kernel
helloHello, World!
init_augmentationGenerate an initial configuration that is concordant with the...
init_config_matinitializes the bookkeeping object for population level...
init_epimodelInitialize epimodel bookkeeping object.
init_irmInitialize an arrays for storing matrices of rates,...
init_obs_matInitializes a bookkeeping object for the observed and...
init_rate_mapConstruct an index matrix identifying with which states each...
init_resultsInitialize list for storing results
init_settingsInitialize a bookkeeping list of MCMC settings.
init_state_lookupInsert a lookup table to map subjects at risk for each...
init_trajectoriesInitialize a set of trajectories if an initial set of paths...
init_tuningInitialize tuning for M-H kernels.
insertPathInsert subject transitions into the population-level and...
insert_rowGeneric function to insert a row into a matrix.
insert_trajectoryInsert a newly sampled subject-level trajectory so its...
irm_decompCompute the eigen decomposition for a rate matrix, and either...
joinCubesJoin two armadillo cubes
logitlogit function
match_rowReturns either a logical vector of indices for which row(s)...
MH_accept_rejectAccept or reject a proposed subject-level trajectory via MH...
mh_templateTemplate for Metropolis-Hastings kernel
normalizeNormalize a vector or matrix.
plot_epimodelPlot the current trajectory and data in an epimodel object...
plot_latent_posteriorPlot the posterior distribution of the latent paths for...
populationLikelihoodGet the irm keys for the compartment counts in a population...
prepare_epimodelPrepares an epimodel environment.
rcpp_helloHello, Rcpp!
reinsert_pathRe-insert the current path back into the configuration...
remove_trajectoryRemove the contribution of a subject from the compartment...
reorderMatReorder the rows of a matrix
resolveSubjContribAdd or remove the subject contribution from the compartment...
retrieveKeysGet the irm keys for the compartment counts in a population...
retrieveSubjPathInsert subject transitions into the population-level and...
sample_at_event_timesSample the infection status at times of state transition of...
sample_at_obs_timesSample the infection status for the specified subject at...
sampleEventSubseqUpdate eigen values, vectors, and inverse matrices for irms
sample_forwardForward path sampling.
sample_pathWrapper for sampling the path within homogeneous intervals.
sim_one_eventSimulate the next event using Gillespie's next reaction...
simulate_epimodelSimulates a stochastic epidemic model.
simulateSIRsimulateSIR function, included in this file because of...
simulate_SIRSimulate an epidemic with SIR dynamics and draw binomial...
subjectLikelihoodGet the irm keys for the compartment counts in a population...
subject_probabilitiesBuild a vector of probabilities according to which subjects...
templatesGenerates a template script for specifying a transition...
tpmProdSeqsUpdate eigen values, vectors, and inverse matrices for irms
tpmSeqsUpdate eigen values, vectors, and inverse matrices for irms
traj_to_obsInstatiates a data matrix based on a configuration matrix....
tune_proposalTune proposal distribution for randow walk M-H parameter...
update_obs_matUpdate the observation matrix and the indices of observation...
update_paramsReplace the vector of parameters in an epimodel object with...
update_tpmsUpdate the list of tpms and tpm products to reflect the...
fintzij/BDAepimodel documentation built on May 14, 2017, 1:18 a.m.