Files in adamkucharski/serosolver
Inference framework for serological data

.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/RcppExports.R R/analysis.R R/beta_binomial_funcs.R R/check_inputs.R R/helpers.R R/mcmc.R R/mcmc_PT_aux_fast.R R/mcmc_PT_fast.R R/mcmc_help.R R/model_wrappers.R R/plots.R R/posteriors.R R/priors.R R/proposal_infection_history.R R/proposal_theta.R R/simulate_cross_sectional.R R/simulate_data.R R/zzz.R README.md build_win.R
build_win.Rr
data/antigenic_maps/antigenicMap_vietnam.csv
data/antigenic_maps/bedford_elife_2014.csv
data/antigenic_maps/created_maps/bedford_annual_continuous.csv
data/antigenic_maps/created_maps/bedford_quarterly.csv
data/antigenic_maps/created_maps/bedford_quarterly_fluscape_cluster_within_cluster.csv
data/antigenic_maps/created_maps/bedford_quarterly_fluscape_cluster_within_year.csv
data/antigenic_maps/created_maps/bedford_vietnam_annual_clustered.csv
data/antigenic_maps/created_maps/fonville_annual_continuous.csv
data/antigenic_maps/created_maps/fonville_quarterly.csv
data/antigenic_maps/created_maps/fonville_quarterly_fluscape_cluster_within_cluster.csv
data/antigenic_maps/created_maps/fonville_quarterly_fluscape_cluster_within_year.csv
data/antigenic_maps/created_maps/fonville_vietnam_annual_clustered.csv
data/antigenic_maps/fluscape_antigenic_map_clustered.csv
data/antigenic_maps/fluscape_map_3monthly.csv
data/antigenic_maps/fluscape_map_6monthly.csv
data/antigenic_maps/fluscape_map_annual.csv
data/antigenic_maps/fluscape_map_monthly.csv
data/antigenic_maps/fonville_clusters.csv
data/antigenic_maps/vietnam_antigenic_coords.csv
data/antigenic_maps/xiangjun2012_clusters.csv
data/fonville_map_approx.csv
data/priors/vietnam_priors.csv
data/real/.~lock.combined_fluscape_data_12.csv#
data/real/HaNam_samples.csv
data/real/fluscape_ages.csv
data/real/fluscape_data_annual.csv
data/real/fluscape_data_annual_original.csv
data/real/fluscape_data_quarterly.csv
data/real/vietnam_ages.csv
data/real/vietnam_data.csv
data/real/vietnam_data_1run.csv
data/real/vietnam_data_primary.csv
data/seasonal.cohort.wane.2_ages.csv
data/seasonal.cohort.wane.2_dat.csv
data/seasonal.cohort.wane.2_infHist.csv
data/simulated/fluscape/clustered_within_cluster/fluscape_sim_quarter_clustered_within_cluster_AR_4.csv
data/simulated/fluscape/clustered_within_cluster/fluscape_sim_quarter_clustered_within_cluster_ages_4.csv
data/simulated/fluscape/clustered_within_cluster/fluscape_sim_quarter_clustered_within_cluster_dat_4.csv
data/simulated/fluscape/clustered_within_cluster/fluscape_sim_quarter_clustered_within_cluster_infHist_4.csv
data/simulated/fluscape/clustered_within_cluster/fluscape_sim_quarter_clustered_within_cluster_pars_4.csv
data/simulated/fluscape/clustered_within_year/fluscape_sim_quarter_clustered_within_year_AR_4.csv
data/simulated/fluscape/clustered_within_year/fluscape_sim_quarter_clustered_within_year_ages_4.csv
data/simulated/fluscape/clustered_within_year/fluscape_sim_quarter_clustered_within_year_dat_4.csv
data/simulated/fluscape/clustered_within_year/fluscape_sim_quarter_clustered_within_year_infHist_4.csv
data/simulated/fluscape/clustered_within_year/fluscape_sim_quarter_clustered_within_year_pars_4.csv
data/simulated/fluscape/fluscape_ages_1.csv
data/simulated/fluscape/fluscape_ages_10.csv
data/simulated/fluscape/fluscape_ages_12.csv
data/simulated/fluscape/fluscape_ages_2.csv
data/simulated/fluscape/fluscape_ages_4.csv
data/simulated/fluscape/fluscape_data_1.csv
data/simulated/fluscape/fluscape_data_10.csv
data/simulated/fluscape/fluscape_data_12.csv
data/simulated/fluscape/fluscape_data_2.csv
data/simulated/fluscape/fluscape_data_4.csv
data/simulated/fluscape/titre_dependent/fluscape_sim_quarter_titredep_AR_4.csv
data/simulated/fluscape/titre_dependent/fluscape_sim_quarter_titredep_ages_4.csv
data/simulated/fluscape/titre_dependent/fluscape_sim_quarter_titredep_dat_4.csv
data/simulated/fluscape/titre_dependent/fluscape_sim_quarter_titredep_infHist_4.csv
data/simulated/fluscape/titre_dependent/fluscape_sim_quarter_titredep_pars_4.csv
data/simulated/sim_1000_AR.csv
data/simulated/sim_1000_ages.csv
data/simulated/sim_1000_data.csv
data/simulated/sim_1000_infHist.csv
data/simulated/sim_1000_titres.csv
data/simulated/sim_1000a_AR.csv
data/simulated/sim_1000a_ages.csv
data/simulated/sim_1000a_data.csv
data/simulated/sim_1000a_infHist.csv
data/simulated/sim_10_AR.csv
data/simulated/sim_10_ages.csv
data/simulated/sim_10_infHist.csv
data/simulated/sim_10_titres.csv
data/simulated/sim_200_AR.csv
data/simulated/sim_200_ages.csv
data/simulated/sim_200_infHist.csv
data/simulated/sim_200_lambda_AR.csv
data/simulated/sim_200_lambda_ages.csv
data/simulated/sim_200_lambda_infHist.csv
data/simulated/sim_200_lambda_titres.csv
data/simulated/sim_200_titres.csv
data/simulated/vietnam/clustered/vietnam_sim_clustered_AR_1.csv
data/simulated/vietnam/clustered/vietnam_sim_clustered_ages_1.csv
data/simulated/vietnam/clustered/vietnam_sim_clustered_dat_1.csv
data/simulated/vietnam/clustered/vietnam_sim_clustered_infHist_1.csv
data/simulated/vietnam/clustered/vietnam_sim_clustered_pars_1.csv
data/simulated/vietnam/titre_dependent/vietnam_sim_titredep_AR_1.csv
data/simulated/vietnam/titre_dependent/vietnam_sim_titredep_ages_1.csv
data/simulated/vietnam/titre_dependent/vietnam_sim_titredep_dat_1.csv
data/simulated/vietnam/titre_dependent/vietnam_sim_titredep_infHist_1.csv
data/simulated/vietnam/titre_dependent/vietnam_sim_titredep_pars_1.csv
data/simulated/vietnam/vietnam_sim_AR_1.csv
data/simulated/vietnam/vietnam_sim_ages_1.csv
data/simulated/vietnam/vietnam_sim_dat_1.csv
data/simulated/vietnam/vietnam_sim_infHist_1.csv
data/simulated/vietnam/vietnam_sim_pars_1.csv
data/simulated/vietnam_data_primary.csv
data/vietnam.csv
data/vietnam_antigenic_coords~
inputs/parTab_base.csv
inputs/parTab_base_titre.csv
inputs/parTab_foi.csv
inputs/parTab_wane.csv
man/add_measurement_shifts.Rd man/add_noise.Rd man/bb_mean.Rd man/bb_var.Rd man/calc_phi_probs.Rd man/calc_phi_probs_indiv.Rd man/calc_phi_probs_indiv_brute.Rd man/calc_phi_probs_monthly.Rd man/calculate_infection_history_statistics.Rd man/calibrate_temperatures.Rd man/check_attack_rates.Rd man/check_data.Rd man/check_par_tab.Rd man/check_proposals.Rd man/create_age_mask.Rd man/create_cross_reactivity_vector.Rd man/create_posterior_func.Rd man/create_posterior_func_fast.Rd man/create_prior_mu.Rd man/create_prob_shifts.Rd man/create_strain_mask.Rd man/db.Rd man/dbb.Rd man/dbb_prior.Rd man/density_beta_binom.Rd man/estimate_mode.Rd man/expand_summary_infChain.Rd man/expand_summary_inf_chain.Rd man/find_bb_2.Rd man/find_beta_parameters.Rd man/find_prior_alpha_beta.Rd man/fit_beta_prior.Rd man/fit_normal_prior.Rd man/fromUnitScale.Rd man/gen_spline_y.Rd man/generate_alpha_beta_prior_mode.Rd man/generate_antigenic_map.Rd man/generate_antigenic_map_flexible.Rd man/generate_ar_annual.Rd man/generate_beta_prior_mean.Rd man/generate_cumulative_inf_plots.Rd man/generate_phis.Rd man/generate_quantiles.Rd man/get_best_pars.Rd man/get_index_pars.Rd man/get_n_alive.Rd man/get_n_alive_location.Rd man/get_titre_predictions.Rd man/get_total_number_infections.Rd man/hist_rbb.Rd man/inf_hist_prob_phi.Rd man/inf_hist_prop_cpp.Rd man/inf_hist_swap.Rd man/inf_hist_swap_phi.Rd man/inf_mat_prior.Rd man/inf_mat_prior_cpp.Rd man/inf_mat_prior_cpp_vector.Rd man/inf_mat_prior_total_cpp.Rd man/infection_history_betabinom.Rd man/infection_history_betabinom_group.Rd man/infection_history_prior.Rd man/infection_history_proposal.Rd man/infection_history_proposal_gibbs.Rd man/infection_history_proposal_gibbs_R.Rd man/infection_history_proposal_gibbs_fast.Rd man/infection_history_symmetric.Rd man/infection_model_indiv.Rd man/likelihood_data_individual.Rd man/likelihood_func_fast.Rd man/likelihood_titre_basic.Rd man/load_antigenic_map_file.Rd man/load_infection_chains.Rd man/load_mcmc_chains.Rd man/load_start_tab.Rd man/load_theta_chains.Rd man/load_titre_dat.Rd man/melt_antigenic_coords.Rd man/mvr_proposal.Rd man/pad_alphas_and_betas.Rd man/pad_inf_chain.Rd man/parallel_tempering.Rd man/pbb.Rd man/phi_proposal.Rd man/plot_attack_rate_residuals.Rd man/plot_attack_rates.Rd man/plot_attack_rates_monthly.Rd man/plot_data.Rd man/plot_infection_histories.Rd man/plot_infection_history_chains_indiv.Rd man/plot_infection_history_chains_time.Rd man/plot_number_infections.Rd man/plot_posteriors_infhist.Rd man/plot_posteriors_theta.Rd man/plot_samples_distances.Rd man/plot_total_number_infections.Rd man/prob_mus.Rd man/prob_shifts.Rd man/protect.Rd man/qbb.Rd man/r_likelihood.Rd man/rbb.Rd man/rm_scale.Rd man/run_MCMC.Rd man/run_MCMC_pt_fast.Rd man/save_infection_history_to_disk.Rd man/scaletuning.Rd man/setup_infection_histories_new.Rd man/setup_infection_histories_new_2.Rd man/setup_infection_histories_old.Rd man/setup_infection_histories_total.Rd man/setup_titredat_for_posterior_func.Rd man/simulate_attack_rates.Rd man/simulate_cross_sectional.Rd man/simulate_data.Rd man/simulate_group.Rd man/simulate_individual.Rd man/simulate_infection_histories.Rd man/solve_model_individual.Rd man/subset_nullable_vector.Rd man/sum_buckets.Rd man/sum_likelihoods.Rd man/titre_data_fast.Rd man/titre_data_group.Rd man/titre_data_individual.Rd man/titre_dependent_boosting_plot.Rd man/to.pdf.Rd man/to.png.Rd man/to.svg.Rd man/toUnitScale.Rd man/univ_proposal.Rd man/wane_function.Rd scripts/AK_simulations.R scripts/main_model.R
scripts/main_real.R~
scripts/minimal_script.R scripts/real/fluscape_full_run.R scripts/real/fluscape_gibbs.R
scripts/real/fluscape_gibbs.R~
scripts/real/fluscape_gibbs_PT.R scripts/real/fluscape_measurement.R scripts/real/fluscape_run.R scripts/real/fluscape_run_mu.R scripts/real/fluscape_titre_dependent.R scripts/real/fluscape_titre_gibbs.R scripts/real/fluscape_with_vietnam_ages.R scripts/sim/prior_infhist_sim.R scripts/sim/sim_gibbs_sampler.R
scripts/sim/sim_gibbs_sampler.R~
scripts/sim/sim_lambda_inference.R scripts/sim/sim_measurement_bias.R scripts/sim/sim_random_mu.R scripts/sim/sim_run.R
scripts/sim/sim_run.R~
scripts/sim/sim_titre_dependent.R scripts/sim/sim_wane_function.R scripts/sim/simulate_data.R scripts/sim/simulate_data_script.R scripts/sim/vietnam_sim_recover.R scripts/utility/combine_vietnam_data_from_list.R scripts/utility/extract_vietnam_data.R scripts/utility/extracting_data.R
src/RcppExports.cpp
src/boosting_functions.cpp
src/boosting_functions.h
src/helpers.cpp
src/helpers.h
src/infection_model.cpp
src/infection_model.h
src/infection_model.h~
src/infection_model_mus.cpp~
src/infection_model_mus.h~
src/likelihood_funcs.cpp
src/likelihood_funcs.h
src/proposal.cpp
src/proposal_mus.cpp~
src/serosolver.dll
src/wane_function.cpp
src/wane_function.h
tests/testdata/fluscape_sim_annual_dat.csv
tests/testdata/fonville_annual_continuous.csv
tests/testdata/fonville_clusters.csv
tests/testdata/par_tab_base.csv
tests/testthat.R
tests/testthat/Rprof.out
tests/testthat/test-fastmodel.R
tests/testthat/test-infectionmodel.R tests/testthat/test.R
tests/testthat/test.R~
vignettes/antigenic_map.tiff
vignettes/parTab.csv
vignettes/plos.csl
vignettes/serosolver-quick_start_guide.Rmd
vignettes/serosolver-quick_start_guide.html
vignettes/serosolver-quick_start_guide.md
vignettes/vignette_references.bib
adamkucharski/serosolver documentation built on April 12, 2019, 2:47 p.m.