Files in fintzij/stemr

Stochastic Epidemic Model Simulation and Estimation

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.development_files/examples_stemr_0.1_ebola_mod/ebola_synth.R .development_files/examples_stemr_0.1_ebola_mod/ebola_synth_pomp.R .development_files/examples_stemr_0.1_ebola_mod/effpop_sir_covg.R .development_files/examples_stemr_0.1_ebola_mod/flu_1seas_nostrat_const_SIR.R .development_files/examples_stemr_0.1_ebola_mod/flu_1seas_nostrat_rw2_SIR.R .development_files/examples_stemr_0.1_ebola_mod/guinea.R .development_files/examples_stemr_0.1_ebola_mod/liberia.R .development_files/examples_stemr_0.1_ebola_mod/sierra_leone.R .development_files/examples_stemr_0.1_ebola_mod/sir_coverage.R .development_files/examples_stemr_0.1_ebola_mod/sir_sinfoi_gmrf_rw1.R .development_files/examples_stemr_0.2/sir_approx_comp_lna.R .development_files/examples_stemr_0.2/sir_gmrf_rw1.R .development_files/examples_stemr_0.2/stemr_betabin.R .development_files/examples_stemr_0.2/stemr_sir.R .development_files/incidence_lna_simulations/rev_sim_01_1wk_durs/process_fcns.R .development_files/incidence_lna_simulations/rev_sim_01_1wk_durs/process_results.R .development_files/incidence_lna_simulations/rev_sim_01_1wk_durs/seir_sim_1.R .development_files/incidence_lna_simulations/rev_sim_01_1wk_durs/seir_sim_4.R .development_files/incidence_lna_simulations/rev_sim_01_1wk_durs/weekly_vs_monthly_res.pdf .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/lna/seir_sim_covid.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/lna/seir_sim_ebola.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/lna/seir_sim_flu.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/ode/seir_sim_covid.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/ode/seir_sim_ebola.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/ode/seir_sim_flu.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/pmmh/seir_sim_covid.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/pmmh/seir_sim_ebola.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/pmmh/seir_sim_flu.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/process_fcns.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/process_results.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_diff/process_results_lna.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/lna/seir_sim_covid.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/lna/seir_sim_ebola.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/lna/seir_sim_flu.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/ode/seir_sim_covid.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/ode/seir_sim_ebola.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/ode/seir_sim_flu.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/pmmh/seir_sim_covid.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/pmmh/seir_sim_ebola.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/pmmh/seir_sim_flu.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/process_fcns.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/process_results.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/process_results_lna.R .development_files/incidence_lna_simulations/rev_sim_02_3dis_long/threedis_res.pdf

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.development_files/oc_covid19/oc_data.csv

.development_files/stick_breaking_state_initializer/explore_stick_breaking_rewrite.R .development_files/stick_breaking_state_initializer/stemr_sir_stick_break.R

.development_files/templates/lna_stan_template.txt

.development_files/tests/betabinomial.R .development_files/tests/minweke_LNA_COOL.R .development_files/tests/minweke_LNA_jointinits_COOL.R .development_files/tests/minweke_initdist_COOL.R .development_files/tests/minweke_mvnmh_COOL.R .development_files/tests/minweke_mvnss_COOL.R .development_files/tests/minweke_tparam.R

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DESCRIPTION

NAMESPACE

R/RcppExports.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/calc_initdist_loglik.R R/calc_param_logprior.R R/census_path.R R/census_path_collection.R R/check_tpar_depends.R R/comp_fcn.R R/emission.R R/fit_stem.R R/forcing.R R/incidence2prevalence.R R/initdist_control.R R/initdist_update.R R/initialize_lna.R R/initialize_ode.R R/insert_initdists.R R/insert_params.R R/interact.R R/is_progressive.R R/lna_control.R R/lna_update.R R/load_lna.R R/load_ode.R R/make_stem.R R/mcmc_kernel.R R/mvnmh_control.R R/mvnmh_update.R R/mvnss_control.R R/mvnss_settings.R R/mvnss_update.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/prepare_initdist_objects.R R/prepare_lna_ess_schedule.R R/prepare_param_blocks.R R/rate.R R/rate_fcns_4_lna.R R/rate_fcns_4_ode.R R/reset_nugget.R R/rsbln.R R/save_ess_rec.R R/save_mcmc_sample.R R/set_params.R R/simulate_stem.R R/stem_dynamics.R R/stem_initializer.R R/stem_measure.R R/stem_parameters.R R/sub_comp_rate.R R/sub_powers.R R/tpar.R R/tpar_control.R R/tparam_update.R R/which_absorbing.R README.Rmd README.md

_pkgdown.yml

data/ebola.rda

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src/.gitignore

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_latent_path.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/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/normalise.cpp

src/propose_lna.cpp

src/propose_lna_approx.cpp

src/propose_mvnmh.cpp

src/rate_update_event.cpp

src/rate_update_tcovar.cpp

src/retrieve_census_path.cpp

src/simulate_gillespie.cpp

src/simulate_r_measure.cpp

src/stemr_types.h

src/stemr_utils.h

vignettes/.gitignore

vignettes/ebola_mod_fig.png

vignettes/ebola_westafrica.Rmd vignettes/stemr.Rmd

fintzij/stemr documentation built on March 25, 2022, 12:25 p.m.