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 |
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