Man pages for fintzij/stemr
Stochastic Epidemic Model Simulation and Estimation

add2vecAdd the contents of one vector to another vector
afss_settingsGenerate a list of settings for automated factor slice...
blocks2covReconstitute a joint kernel covariance matrix from block...
build_census_pathConstruct a matrix containing the compartment counts at a...
build_flowmatGiven a list of (unparsed) rate functions, construct the...
build_measproc_indmatConstruct an indicator matrix for which measurement process...
build_obsmatGenerate a template for a stemr observation matrix, or...
build_rate_adjmatConstruct an adjacency matrix for specifying which rates must...
build_tcovar_adjmatConstruct an adjacency matrix for which rates need to be...
build_tcovar_changematIndicator matrix for determining which time-varying...
build_tcovar_matrixConstruct a time-varying covariance matrix that includes time...
CALL_D_MEASUREEvaluate the log-density of the measurement process by...
CALL_INTEGRATE_STEM_ODEIntegrate a system of ODEs via external Xptr.
CALL_RATE_FCNUpdate rates by calling rate functions via Xptr.
CALL_R_MEASURESimulate from the measurement process by calling measurement...
CALL_SET_ODE_PARAMSSet the parameters for a system of ODEs via XPtr.
census_incidenceConstruct a matrix containing the incidence counts at a...
census_lnaConstruct a matrix containing the compartment counts and the...
census_pathWrapper for evaluating the compartment counts at census...
census_path_collectionCensus each path in a collection of paths to obtain the...
comp_cholCholesky decomposition
comp_fcnParses a function of each of a vector of model compartments...
compute_incidenceDifference an incidence variable in a census matrix.
compute_lna_logliksCompute the LNA log likelihood and data log likelihood.
construct_initdist_prior_lnaConstruct a function for evaluating the log prior density of...
construct_initdist_sampler_lnaConstruct a function for sampling new initial compartment...
convert_lna2Convert an LNA path from the counting process on transition...
copy_2_rowsCopy some of the rows of one matrix into another
copy_colCopy the contents of one matrix into another
copy_elemCopy an element from one vector into another
copy_elem2Copy an multiple elements from one vector into another
copy_matCopy the contents of one matrix into another
copy_pathmatCopy the columns of one matrix into another
copy_vecCopy the contents of one vector into another
dmvtnMultivariate normal density
draw_normalsDraw new N(0,1) values and fill a vector.
draw_normals2Draw new N(0,1) values and fill a matrix.
emissionGenerates an emission list to be supplied to the...
ess_settingsGenerates a list of settings for sampling the latent LNA...
evaluate_d_measureEvaluate the log-density of the measurement process by...
evaluate_d_measure_LNAEvaluate the log-density of a possibly time-verying...
expitExpit transformation, i.e. inverse logit
factor_slice_samplerUpdate model parameters via factor slice sampling
factor_slice_sampler_odeUpdate model parameters via factor slice sampling
find_intervalGiven a vector of interval endpoints 'breaks', determine in...
forcingDeclare a time varying covariate to be a forcing variable...
generate_rw1Generate objects for setting up a random walk of order 1
generate_rw2Generate objects for setting up a random walk of order 2
generate_rw3Generate objects for setting up a random walk of order 3
g_prop2c_propGet componentwise proposals from a global proposal.
harss_settingsGenerate a list of settings for automated factor slice...
helloHello, World!
hit_and_run_slice_samplerUpdate model parameters via factor slice sampling
hit_and_run_slice_sampler_odeUpdate model parameters via factor slice sampling
increment_elemIncrement an element of a vector by 1
initialize_lnaInitialize the LNA path
initialize_odeInitialize the LNA path
insert_blockInsert one matrix into another
insert_tparamInsert time-varying parameters into a tcovar matrix.
integrate_odesObtain the path of the deterministic mean of a stochastic...
interactInteract character vectors to get a character vector of...
is_progressiveDetermines whether a model is progressive based on its flow...
kernelSpecify an MCMC transition kernel for updating the model...
lna_incid2prevConvert an LNA path from the counting process on transition...
load_lnaConstruct and compile the functions for proposing an LNA...
load_odeConstruct and compile the functions for proposing an ODE...
logitLogit tranformation
map_draws_2_lnaMap N(0,1) stochastic perturbations to an LNA path.
map_pars_2_odeMap parameters to the deterministic mean incidence increments...
mat_2_arrCopy a matrix into a slice of an array
maximize_loglik_odeObtain estimates of stochastic epidemic model (SEM)...
minimize_sse_odeObtain estimates of stochastic epidemic model (SEM)...
mvn_g_adaptiveGlobal Metropolis random walk with global adaptive scaling
mvn_rwRandom walk Metropolis-Hastings transition kernel.
mvn_slice_samplerUpdate model parameters via factor slice sampling
mvn_slice_sampler_odeUpdate model parameters via factor slice sampling
mvnss_settingsGenerate a list of settings for automated factor slice...
normalisenormalise a vector in place
normalise2return a normalised vector
parblockDefine a parameter block for an MCMC kernel
pars2lnaparsIdentify which rates to update when a state transition event...
parse_lna_ratesParse the LNA rates so they can be compiled.
parse_meas_procsInstatiate the C++ emission probability functions for...
parse_ode_ratesParse the ODE rates so they can be compiled.
parse_parameter_blocksGenerate a list of objects used in block updating MCMC...
parse_rates_exactInstatiate the C++ rate functions for a stochastic epidemic...
plot_adaptationsPlot the adaptation schedule for an adaptive MCMC algorithm...
propose_lnaSimulate an LNA path using a non-centered parameterization...
propose_lna_approxSimulate an approximate LNA path using a non-centered...
rateGenerates a rate list to be supplied to the 'stem_dynamics'...
rate_fcns_4_lnaConvert unparsed rate functions into rate functions...
rate_fcns_4_odeConvert unparsed rate functions into deterministic mean ODE...
rate_update_eventIdentify which rates to update when a state transition event...
rate_update_tcovarIdentify which rates to update based on changes in the...
rcpp_helloHello, Rcpp!
reset_nuggetReset the nugget based based on a sample
reset_slice_ratiosReset counters for interval expansions/contractions and slice...
reset_vecReset a vector by filling it with zeros
retrieve_census_pathInsert the compartment counts at a sequence of census times...
rmvtnProduce samples from a multivariate normal density using the...
sample_unit_sphereSample the unit sphere.
set_paramsSet the parameter values for a stochastic epidemic model...
simulate_gillespieSimulate a stochastic epidemic model path via Gillespie's...
simulate_r_measureSimulate a data matrix from the measurement process of a...
simulate_stemSimulations from a stochastic epidemic model.
stemConstruct a stem object.
stem_dynamicsGenerate the objects governing the dynamics of a stochastic...
stem_inferencePerform inference for a stochastic epidemic model using...
stem_inference_lnaApproximate Bayesian inference for a stochastic epidemic...
stem_inference_odeApproximate Bayesian inference for a stochastic epidemic...
stem_initializerDetermines the initial state probabilities or concentrations...
stem_measureGenerate a list of objects governing the measurement process...
sub_comp_rateMakes comp_fcn replacements.
sub_powersParse a string and substitute powers of the form a^b with...
t0_kernelSpecify the prior for t0 and the standard deviation of the...
tparGenerate a list to be used in specifying a time-varying...
update_factorsUpdate slice factor directions for automated factor slice...
update_interval_widthsUpdate factors and interval widths for automated factor slice...
update_lna_pathSample a new LNA path via elliptical slice sampling.
update_tparamUpdate time-varying parameters via elliptical slice sampling.
update_tparam_odeUpdate time-varying parameters via elliptical slice sampling.
which_absorbingDetects which states in a model are absorbing states
fintzij/stemr documentation built on June 19, 2018, 12:13 a.m.