Files in fintzij/stemr
Stochastic Epidemic Model Simulation and Estimation

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/RcppExports.R R/afss_settings.R R/auxilliary_functions.R R/blocks2cov.R R/build_flowmat.R R/build_measproc_indmat.R R/build_obsmat.R R/build_rate_adjmat.R R/build_tcovar_adjmat.R R/build_tcovar_changemat.R R/build_tcovar_matrix.R R/census_path.R R/census_path_collection.R R/comp_fcn.R R/construct_initdist_prior_lna.R R/construct_initdist_sampler_lna.R R/emission.R R/ess_settings.R R/factor_slice_sampler.R R/factor_slice_sampler_ode.R R/forcing.R R/generate_rw1.R R/generate_rw2.R R/generate_rw3.R R/harss_settings.R R/hit_and_run_slice_sampler.R R/hit_and_run_slice_sampler_ode.R R/incidence2prevalence.R R/initialize_lna.R R/initialize_ode.R R/interact.R R/is_progressive.R R/kernel.R R/load_lna.R R/load_ode.R R/mvn_slice_sampler.R R/mvn_slice_sampler_ode.R R/mvnss_settings.R R/parblock.R R/parse_lna_rates.R R/parse_meas_procs.R R/parse_ode_rates.R R/parse_parameter_blocks.R R/parse_rates_exact.R R/plot_adaptations.R R/rate.R R/rate_fcns_4_lna.R R/rate_fcns_4_ode.R R/reset_nugget.R R/set_params.R R/simulate_stem.R R/stem.R R/stem_dynamics.R R/stem_inference.R R/stem_inference_lna.R R/stem_inference_ode.R R/stem_initializer.R R/stem_measure.R R/sub_comp_rate.R R/sub_powers.R R/t0_kernel.R R/tpar.R R/update_initdist_lna.R R/update_initdist_ode.R R/update_lna_path.R R/update_tparam_lna.R R/update_tparam_ode.R R/which_absorbing.R README.Rmd README.md
inst/templates/lna_stan_template.txt
man/CALL_D_MEASURE.Rd man/CALL_INTEGRATE_STEM_ODE.Rd man/CALL_RATE_FCN.Rd man/CALL_R_MEASURE.Rd man/CALL_SET_ODE_PARAMS.Rd man/add2vec.Rd man/afss_settings.Rd man/blocks2cov.Rd man/build_census_path.Rd man/build_flowmat.Rd man/build_measproc_indmat.Rd man/build_obsmat.Rd man/build_rate_adjmat.Rd man/build_tcovar_adjmat.Rd man/build_tcovar_changemat.Rd man/build_tcovar_matrix.Rd man/census_incidence.Rd man/census_lna.Rd man/census_path.Rd man/census_path_collection.Rd man/comp_chol.Rd man/comp_fcn.Rd man/compute_incidence.Rd man/construct_initdist_prior_lna.Rd man/construct_initdist_sampler_lna.Rd man/convert_lna2.Rd man/copy_2_rows.Rd man/copy_col.Rd man/copy_elem.Rd man/copy_elem2.Rd man/copy_mat.Rd man/copy_pathmat.Rd man/copy_vec.Rd man/copy_vec2.Rd man/dmvtn.Rd man/draw_normals.Rd man/draw_normals2.Rd man/emission.Rd man/ess_settings.Rd man/evaluate_d_measure.Rd man/evaluate_d_measure_LNA.Rd man/expit.Rd man/factor_slice_sampler.Rd man/factor_slice_sampler_ode.Rd man/find_interval.Rd man/forcing.Rd man/g_prop2c_prop.Rd man/generate_rw1.Rd man/generate_rw2.Rd man/generate_rw3.Rd man/harss_settings.Rd man/hello.Rd man/hit_and_run_slice_sampler.Rd man/hit_and_run_slice_sampler_ode.Rd man/incidence2prevalence.Rd man/increment_elem.Rd man/initialize_lna.Rd man/initialize_ode.Rd man/insert_block.Rd man/insert_tparam.Rd man/integrate_odes.Rd man/interact.Rd man/is_progressive.Rd man/kernel.Rd man/lna_incid2prev.Rd man/load_lna.Rd man/load_ode.Rd man/logit.Rd man/map_draws_2_lna.Rd man/map_pars_2_ode.Rd man/mat_2_arr.Rd man/mvn_g_adaptive.Rd man/mvn_rw.Rd man/mvn_slice_sampler.Rd man/mvn_slice_sampler_ode.Rd man/mvnss_settings.Rd man/normalise.Rd man/normalise2.Rd man/parblock.Rd man/pars2lnapars.Rd man/pars2lnapars2.Rd man/parse_lna_rates.Rd man/parse_meas_procs.Rd man/parse_ode_rates.Rd man/parse_parameter_blocks.Rd man/parse_rates_exact.Rd man/plot_adaptations.Rd man/propose_lna.Rd man/propose_lna_approx.Rd man/rate.Rd man/rate_fcns_4_lna.Rd man/rate_fcns_4_ode.Rd man/rate_update_event.Rd man/rate_update_tcovar.Rd man/rcpp_hello.Rd man/reset_nugget.Rd man/reset_slice_ratios.Rd man/reset_vec.Rd man/retrieve_census_path.Rd man/rmvtn.Rd man/sample_unit_sphere.Rd man/set_params.Rd man/simulate_gillespie.Rd man/simulate_r_measure.Rd man/simulate_stem.Rd man/stem.Rd man/stem_dynamics.Rd man/stem_inference.Rd man/stem_inference_lna.Rd man/stem_inference_ode.Rd man/stem_initializer.Rd man/stem_measure.Rd man/sub_comp_rate.Rd man/sub_powers.Rd man/t0_kernel.Rd man/tpar.Rd man/update_factors.Rd man/update_initdist_lna.Rd man/update_initdist_ode.Rd man/update_interval_widths.Rd man/update_lna_path.Rd man/update_tparam_lna.Rd man/update_tparam_ode.Rd man/which_absorbing.Rd
src/CALL_D_MEASURE.cpp
src/CALL_INTEGRATE_STEM_ODE.cpp
src/CALL_RATE_FCN.cpp
src/CALL_R_MEASURE.cpp
src/CALL_SET_ODE_PARAMS.cpp
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/build_census_path.cpp
src/census_incidence.cpp
src/census_lna.cpp
src/compute_incidence.cpp
src/convert_lna2.cpp
src/copy_fcns.cpp
src/draw_normals.cpp
src/evaluate_d_measure.cpp
src/evaluate_d_measure_LNA.cpp
src/find_interval.cpp
src/g_prop2c_prop.cpp
src/insert_tparam.cpp
src/integrate_odes.cpp
src/lna_incid2prev.cpp
src/map_draws_2_lna.cpp
src/map_pars_2_ode.cpp
src/matrix_decompositions.cpp
src/multivariate_normal_fcns.cpp
src/mvn_g_adaptive.cpp
src/mvn_rw.cpp
src/normalise.cpp
src/propose_lna.cpp
src/propose_lna_approx.cpp
src/rate_update_event.cpp
src/rate_update_tcovar.cpp
src/reset_slice_ratios.cpp
src/retrieve_census_path.cpp
src/simulate_gillespie.cpp
src/simulate_r_measure.cpp
src/stemr_types.h
src/stemr_utils.h
src/update_factors.cpp
src/update_interval_widths.cpp
fintzij/stemr documentation built on Dec. 12, 2018, 8:10 a.m.