Man pages for fintzij/stemr
Stochastic Epidemic Model Simulation and Estimation
| add2vec | Add the contents of one vector to another vector |
| blocks2cov | Reconstitute a joint kernel covariance matrix from block... |
| build_census_path | Construct a matrix containing the compartment counts at a... |
| build_flowmat | Given a list of (unparsed) rate functions, construct the... |
| build_measproc_indmat | Construct an indicator matrix for which measurement process... |
| build_obsmat | Generate a template for a stemr observation matrix, or... |
| build_rate_adjmat | Construct an adjacency matrix for specifying which rates must... |
| build_tcovar_adjmat | Construct an adjacency matrix for which rates need to be... |
| build_tcovar_changemat | Indicator matrix for determining which time-varying... |
| build_tcovar_matrix | Construct a time-varying covariance matrix that includes time... |
| calc_initdist_loglik | Return the log-lik of initial distribution draws |
| calc_params_logprior | Return the log prior density over all parameter blocks |
| CALL_D_MEASURE | Evaluate the log-density of the measurement process by... |
| CALL_INTEGRATE_STEM_ODE | Integrate a system of ODEs via external Xptr. |
| CALL_RATE_FCN | Update rates by calling rate functions via Xptr. |
| CALL_R_MEASURE | Simulate from the measurement process by calling measurement... |
| CALL_SET_ODE_PARAMS | Set the parameters for a system of ODEs via XPtr. |
| census_incidence | Construct a matrix containing the incidence counts at a... |
| census_latent_path | Construct a matrix containing the compartment counts and the... |
| census_path | Wrapper for evaluating the compartment counts at census... |
| census_path_collection | Census each path in a collection of paths to obtain the... |
| check_tpar_depends | Check if time varying parameters depend on initial conditions |
| comp_chol | Cholesky decomposition |
| comp_fcn | Parses a function of each of a vector of model compartments... |
| compute_incidence | Difference an incidence variable in a census matrix. |
| convert_lna2 | Convert an LNA path from the counting process on transition... |
| copy_2_rows | Copy some of the rows of one matrix into another |
| copy_col | Copy the contents of one matrix into another |
| copy_elem | Copy an element from one vector into another |
| copy_elem2 | Copy an multiple elements from one vector into another |
| copy_mat | Copy the contents of one matrix into another |
| copy_pathmat | Copy the columns of one matrix into another |
| copy_row | Copy the contents of one matrix into another |
| copy_vec | Copy the contents of one vector into another |
| copy_vec2 | Copy the contents of one vector into another |
| dmvtn | Multivariate normal density |
| draw_normals | Draw new N(0,1) values and fill a vector. |
| draw_normals2 | Draw new N(0,1) values and fill a matrix. |
| emission | Generates an emission list to be supplied to the... |
| evaluate_d_measure | Evaluate the log-density of the measurement process by... |
| evaluate_d_measure_LNA | Evaluate the log-density of a possibly time-verying... |
| expit | Expit transformation, i.e. inverse logit |
| find_interval | Given a vector of interval endpoints 'breaks', determine in... |
| fit_stem | Fit a stochastic epidemic model using the linear noise... |
| forcing | Declare a time varying covariate to be a forcing variable... |
| hello | Hello, World! |
| incidence2prevalence | Convert an LNA/ODE incidence path to a prevalence path. |
| increment_elem | Increment an element of a vector by 1 |
| increment_vec | Add one vector to another |
| initdist_control | Generates a list of settings for sampling the latent LNA... |
| initdist_update | Sample a new LNA path via elliptical slice sampling. |
| initialize_lna | Initialize the LNA path |
| initialize_ode | Initialize the ODE path |
| insert_block | Insert one matrix into another |
| insert_elem | insert an element into a vector |
| insert_initdist | Insert natural scale parameters into a parameter matrix |
| insert_params | Insert natural scale parameters into a parameter matrix |
| insert_tparam | Insert time-varying parameters into a tcovar matrix. |
| integrate_odes | Obtain the path of the deterministic mean of a stochastic... |
| interact | Interact character vectors to get a character vector of... |
| is_progressive | Determines whether a model is progressive based on its flow... |
| lna_control | Generates a list of settings for sampling the latent LNA... |
| lna_incid2prev | Convert an LNA path from the counting process on transition... |
| lna_update | Sample a new LNA path via elliptical slice sampling. |
| load_lna | Construct and compile the functions for proposing an LNA... |
| load_ode | Construct and compile the functions for proposing an ODE... |
| logit | Logit tranformation |
| make_stem | Construct a stem object. |
| map_draws_2_lna | Map N(0,1) stochastic perturbations to an LNA path. |
| map_pars_2_ode | Map parameters to the deterministic mean incidence increments... |
| mat_2_arr | Copy a matrix into a slice of an array |
| mcmc_kernel | Specify an MCMC transition kernel |
| mvnmh_control | Generate a list of settings for Metropolis-Hastings updates... |
| mvnmh_update | Multivariate normal Metropolis-Hastings update |
| mvnss_control | Generate a list of settings for multivariate normal slice... |
| mvnss_settings | Generate a list of settings for automated factor slice... |
| mvnss_update | Update model parameters via factor slice sampling |
| normalise | normalise a vector in place |
| normalise2 | return a normalised vector |
| parblock | Define a parameter block for an MCMC kernel |
| pars2lnapars | Insert parameters into each row of a parameter matrix |
| pars2lnapars2 | Insert parameters into the first row of a parameter matrix |
| pars2parmat | Insert parameters into the first row of a parameter matrix |
| parse_lna_rates | Parse the LNA rates so they can be compiled. |
| parse_meas_procs | Instatiate the C++ emission probability functions for... |
| parse_ode_rates | Parse the ODE rates so they can be compiled. |
| parse_parameter_blocks | Generate a list of objects used in block updating MCMC... |
| parse_rates_exact | Instatiate the C++ rate functions for a stochastic epidemic... |
| plot_adaptations | Plot the adaptation schedule for an adaptive MCMC algorithm... |
| prepare_initdist_objects | Prepare initial distribution list for MCMC |
| prepare_lna_ess_schedule | Prepare an LNA elliptical slice sampling schedule |
| prepare_param_blocks | Prepare the parameter blocks for MCMC |
| propose_lna | Simulate an LNA path using a non-centered parameterization... |
| propose_lna_approx | Simulate an approximate LNA path using a non-centered... |
| propose_mvnmh | Multivariate normal Metropolis-Hastings proposal |
| rate | Generates a rate list to be supplied to the 'stem_dynamics'... |
| rate_fcns_4_lna | Convert unparsed rate functions into rate functions... |
| rate_fcns_4_ode | Convert unparsed rate functions into deterministic mean ODE... |
| rate_update_event | Identify which rates to update when a state transition event... |
| rate_update_tcovar | Identify which rates to update based on changes in the... |
| rcpp_hello | Hello, Rcpp! |
| reset_nugget | Reset the nugget based based on a sample |
| reset_vec | Reset a vector by filling it with an element |
| retrieve_census_path | Insert the compartment counts at a sequence of census times... |
| rmvtn | Produce samples from a multivariate normal density using the... |
| rsbln | Stick-Breaking Logit-Normal |
| sample_unit_sphere | Sample the unit sphere. |
| save_ess_rec | Save the elliptical slice sampling record |
| save_mcmc_sample | Save an MCMC sample |
| sbln_explorer | Stick-Breaking Logit-Normal Explorer |
| sbln_normal_to_volume | Convert Normal Draws to Stick-Breaking Logit-Normal Draws |
| set_params | Set the parameter values for a stochastic epidemic model... |
| simulate_gillespie | Simulate a stochastic epidemic model path via Gillespie's... |
| simulate_r_measure | Simulate a data matrix from the measurement process of a... |
| simulate_stem | Simulations from a stochastic epidemic model. |
| stem_dynamics | Generate the objects governing the dynamics of a stochastic... |
| stem_initializer | Determines the initial state probabilities or concentrations... |
| stem_measure | Generate a list of objects governing the measurement process... |
| stem_parameters | Assign a vector of parameters to a stem object |
| sub_comp_rate | Makes comp_fcn replacements. |
| sub_powers | Parse a string and substitute powers of the form a^b with... |
| tpar | Generate a list to be used in specifying a time-varying... |
| tparam_update | Sample a new LNA path via elliptical slice sampling. |
| tpar_control | Generates a list of settings for sampling the latent LNA... |
| vec_2_arr | Copy a matrix into a column of a slice of an array |
| vec_2_mat | Copy a vector into a matrix |
| which_absorbing | Detects which states in a model are absorbing states |
