Files in seroanalytics/serosolver
Inference Framework for Serological Data

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

Meta/vignette.rds

NAMESPACE

R/RcppExports.R R/analysis.R R/check_inputs.R R/data.R R/helpers.R R/infection_model_likelihoods.R R/mcmc.R R/mcmc_help.R R/observation_model_likelihoods.R R/plot_antibody_model.R R/plot_infection_histories.R R/plots_other.R R/posteriors.R R/priors.R R/proposal_infection_history.R R/proposal_theta.R R/simulate_data.R R/zzz.R README.Rmd README.md

_config.yml

codemeta.json

data/cs1_chains_real.RData

data/cs1_chains_real_b.RData

data/cs1_chains_sim.RData

data/cs2_chains_real.RData

data/cs2_chains_real_b.RData

data/cs2_chains_sim.RData

data/example_antibody_data.RData

data/example_antigenic_map.RData

data/example_inf_chain.RData

data/example_inf_hist.RData

data/example_par_tab.RData

data/example_theta_chain.RData

doc/cs1_vignette.html

doc/cs2_vignette.html

doc/serosolver-quick_start_guide.html

docs/404.html

docs/LICENSE-text.html

docs/articles/cs1_vignette.html

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docs/articles/cs2_vignette.html

docs/articles/cs2_vignette_files/figure-html/age_clusters_plot-1.png

docs/articles/cs2_vignette_files/figure-html/age_distribution-1.png

docs/articles/cs2_vignette_files/figure-html/attack_rate_plot-1.png

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docs/articles/cs2_vignette_files/figure-html/unnamed-chunk-8-1.png

docs/articles/index.html

docs/articles/serosolver-quick_start_guide.html

docs/authors.html

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/add_measurement_shifts.html

docs/reference/add_noise.html

docs/reference/bb_mean.html

docs/reference/bb_var.html

docs/reference/calc_phi_probs.html

docs/reference/calc_phi_probs_indiv.html

docs/reference/calc_phi_probs_spline.html

docs/reference/calculate_infection_history_statistics.html

docs/reference/check_attack_rates.html

docs/reference/check_data.html

docs/reference/check_inf_hist.html

docs/reference/check_par_tab.html

docs/reference/check_proposals.html

docs/reference/create_age_mask.html

docs/reference/create_cross_reactivity_vector.html

docs/reference/create_posterior_func.html

docs/reference/create_prior_mu.html

docs/reference/create_prob_shifts.html

docs/reference/create_strain_mask.html

docs/reference/cs1_chains_real.html

docs/reference/cs1_chains_real_b.html

docs/reference/cs1_chains_sim.html

docs/reference/cs2_chains_real.html

docs/reference/cs2_chains_real_b.html

docs/reference/cs2_chains_sim.html

docs/reference/db.html

docs/reference/dbb.html

docs/reference/dbb_prior.html

docs/reference/density_beta_binom.html

docs/reference/describe_priors.html

docs/reference/estimate_mode.html

docs/reference/example_antigenic_map.html

docs/reference/example_inf_chain.html

docs/reference/example_inf_hist.html

docs/reference/example_par_tab.html

docs/reference/example_theta_chain.html

docs/reference/example_titre_dat.html

docs/reference/expand_summary_infChain.html

docs/reference/expand_summary_inf_chain.html

docs/reference/figures/README-example-1.png

docs/reference/find_bb_2.html

docs/reference/find_beta_prior_mode.html

docs/reference/find_beta_prior_with_mean.html

docs/reference/find_beta_prior_with_mean_var.html

docs/reference/find_prior_alpha_beta.html

docs/reference/fit_beta_prior.html

docs/reference/fit_normal_prior.html

docs/reference/fromUnitScale.html

docs/reference/gen_spline_y.html

docs/reference/generate_antigenic_map.html

docs/reference/generate_antigenic_map_flexible.html

docs/reference/generate_ar_annual.html

docs/reference/generate_cumulative_inf_plots.html

docs/reference/generate_phis.html

docs/reference/generate_quantiles.html

docs/reference/generate_start_tab.html

docs/reference/get_DOBs.html

docs/reference/get_best_pars.html

docs/reference/get_index_pars.html

docs/reference/get_n_alive.html

docs/reference/get_n_alive_group.html

docs/reference/get_titre_predictions.html

docs/reference/get_total_number_infections.html

docs/reference/hist_rbb-1.png

docs/reference/hist_rbb.html

docs/reference/index.html

docs/reference/inf_hist_prop_prior_v2_and_v4.html

docs/reference/inf_hist_prop_prior_v3.html

docs/reference/inf_hist_swap.html

docs/reference/inf_hist_swap_phi.html

docs/reference/inf_mat_prior.html

docs/reference/inf_mat_prior_cpp.html

docs/reference/inf_mat_prior_cpp_vector.html

docs/reference/inf_mat_prior_group_cpp.html

docs/reference/inf_mat_prior_group_cpp_vector.html

docs/reference/inf_mat_prior_total_group_cpp.html

docs/reference/infection_history_prior.html

docs/reference/infection_history_symmetric.html

docs/reference/likelihood_func_fast.html

docs/reference/load_antigenic_map_file.html

docs/reference/load_infection_chains.html

docs/reference/load_mcmc_chains.html

docs/reference/load_start_tab.html

docs/reference/load_theta_chains.html

docs/reference/load_titre_dat.html

docs/reference/melt_antigenic_coords.html

docs/reference/mvr_proposal.html

docs/reference/pad_alphas_and_betas.html

docs/reference/pad_inf_chain.html

docs/reference/pbb.html

docs/reference/plot_attack_rates.html

docs/reference/plot_attack_rates_monthly.html

docs/reference/plot_data.html

docs/reference/plot_infection_histories.html

docs/reference/plot_infection_history_chains_indiv.html

docs/reference/plot_infection_history_chains_time.html

docs/reference/plot_number_infections.html

docs/reference/plot_posteriors_infhist.html

docs/reference/plot_posteriors_theta.html

docs/reference/plot_samples_distances.html

docs/reference/plot_total_number_infections.html

docs/reference/prob_mus.html

docs/reference/prob_shifts.html

docs/reference/protect.html

docs/reference/qbb.html

docs/reference/r_likelihood.html

docs/reference/rbb.html

docs/reference/rm_scale.html

docs/reference/run_MCMC.html

docs/reference/save_infection_history_to_disk.html

docs/reference/scaletuning.html

docs/reference/setup_infection_histories.html

docs/reference/setup_infection_histories_new.html

docs/reference/setup_infection_histories_new_2.html

docs/reference/setup_infection_histories_old.html

docs/reference/setup_infection_histories_titre.html

docs/reference/setup_infection_histories_total.html

docs/reference/setup_titredat_for_posterior_func.html

docs/reference/simulate_attack_rates.html

docs/reference/simulate_cross_sectional.html

docs/reference/simulate_data.html

docs/reference/simulate_group.html

docs/reference/simulate_individual.html

docs/reference/simulate_individual_faster.html

docs/reference/simulate_infection_histories.html

docs/reference/subset_nullable_vector.html

docs/reference/sum_buckets.html

docs/reference/sum_infections_by_group.html

docs/reference/sum_likelihoods.html

docs/reference/titre_data_fast.html

docs/reference/titre_dependent_boosting_plot.html

docs/reference/to.pdf.html

docs/reference/to.png.html

docs/reference/to.svg.html

docs/reference/toUnitScale.html

docs/reference/univ_proposal.html

docs/reference/wane_function.html

inst/CITATION

inst/extdata/FluScape_YOB.csv

inst/extdata/Fluscape_HI_NT_titres.csv

inst/extdata/Fluscape_HI_data.csv

inst/extdata/Fluscape_SupplmentalDataS1.csv

inst/extdata/HKdata_h1n1_unvac.csv

inst/extdata/HKdata_h1n1_vac.csv

inst/extdata/antigenic_map.tiff

inst/extdata/antigenic_maps/antigenicMap_vietnam.csv

inst/extdata/antigenic_maps/bedford_elife_2014.csv

inst/extdata/antigenic_maps/fonville_clusters.csv

inst/extdata/antigenic_maps/fonville_map_approx.csv

inst/extdata/antigenic_maps/vietnam_antigenic_coords.csv

inst/extdata/antigenic_maps/xiangjun2012_clusters.csv

inst/extdata/bmc_isolate_data.csv

inst/extdata/cs1_real/.blank

inst/extdata/cs1_sim/.blank

inst/extdata/cs2_real/.blank

inst/extdata/cs2_sim/.blank

inst/extdata/fonville_clusters.csv

inst/extdata/fonville_map_approx.csv

inst/extdata/par_tab_base.csv

inst/extdata/priors/vietnam_priors.csv

inst/extdata/readme/create_example_data.R

inst/extdata/real/HaNam_samples.csv

inst/extdata/real/vietnam_ages.csv

inst/extdata/real/vietnam_data.csv

inst/extdata/xiangjun2012_clusters.csv

man/Fast-observation-error-function-continuous.Rd man/add_measurement_shifts.Rd man/add_noise.Rd man/antibody_model.Rd man/calc_phi_probs.Rd man/calc_phi_probs_indiv.Rd man/calc_phi_probs_spline.Rd man/calculate_infection_history_statistics.Rd man/check_attack_rates.Rd man/check_data.Rd man/check_inf_hist.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_prob_shifts.Rd man/create_sample_mask.Rd man/create_start_level_data.Rd man/cs1_chains_real.Rd man/cs1_chains_real_b.Rd man/cs1_chains_sim.Rd man/cs2_chains_real.Rd man/cs2_chains_real_b.Rd man/cs2_chains_sim.Rd man/db.Rd man/dbb_prior.Rd man/density_beta_binom.Rd man/describe_priors.Rd man/estimate_mode.Rd man/example_antibody_data.Rd man/example_antigenic_map.Rd man/example_inf_chain.Rd man/example_inf_hist.Rd man/example_par_tab.Rd man/example_theta_chain.Rd man/expand_summary_inf_chain.Rd

man/figures/README-example-1.png

man/figures/README-example-2.png

man/figures/README-example-3.png

man/figures/README-example_mcmc-1.png

man/figures/README-example_model_fits-1.png

man/figures/README-example_plot-1.png

man/find_beta_prior_mode.Rd man/find_beta_prior_with_mean.Rd man/find_beta_prior_with_mean_var.Rd man/fit_beta_prior.Rd man/fit_normal_prior.Rd man/fromUnitScale.Rd man/gen_spline_y.Rd man/generate_antigenic_map_flexible.Rd man/generate_phis.Rd man/generate_quantiles.Rd man/generate_start_tab.Rd man/get_DOBs.Rd man/get_antibody_level_predictions.Rd man/get_best_pars.Rd man/get_index_pars.Rd man/get_n_alive.Rd man/get_n_alive_group.Rd man/get_total_number_infections.Rd man/identify_run_lengths.Rd man/inf_hist_prop_prior_v2_and_v4.Rd man/inf_hist_prop_prior_v3.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_group_cpp.Rd man/inf_mat_prior_group_cpp_vector.Rd man/inf_mat_prior_total_group_cpp.Rd man/infection_history_prior.Rd man/infection_history_symmetric.Rd man/likelihood_func_fast.Rd man/load_antibody_data.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/melt_antigenic_coords.Rd man/mvr_proposal.Rd man/pad_inf_chain.Rd man/pad_infection_model_prior_parameters.Rd man/plot_antibody_data.Rd man/plot_antibody_dependent_boosting.Rd man/plot_antibody_model.Rd man/plot_antibody_predictions.Rd man/plot_attack_rates.Rd man/plot_attack_rates_pointrange.Rd man/plot_cumulative_infection_histories.Rd man/plot_estimated_antibody_model.Rd man/plot_individual_number_infections.Rd man/plot_infection_history_chains_indiv.Rd man/plot_infection_history_chains_time.Rd man/plot_model_fits.Rd man/plot_posteriors_infhist.Rd man/plot_samples_distances.Rd man/plot_total_number_infections.Rd man/prob_shifts.Rd man/protect.Rd man/protect_posterior.Rd man/r_likelihood.Rd man/r_likelihood_continuous.Rd man/rm_scale.Rd man/save_infection_history_to_disk.Rd man/scaletuning.Rd man/serosolver.Rd man/setup_antibody_data_for_posterior_func.Rd man/setup_infection_histories.Rd man/setup_infection_histories_antibody_level.Rd man/setup_infection_histories_prior.Rd man/simulate_antibody_model.Rd man/simulate_attack_rates.Rd man/simulate_data.Rd man/simulate_infection_histories.Rd man/subset_nullable_vector.Rd man/sum_buckets.Rd man/sum_infections_by_group.Rd man/sum_likelihoods.Rd man/summarize_run_lengths.Rd man/to.pdf.Rd man/to.png.Rd man/to.svg.Rd man/toUnitScale.Rd man/univ_proposal.Rd man/unregister_dopar.Rd

src/RcppExports.cpp

src/antibody_models.cpp

src/antibody_models_individual.cpp

src/antibody_models_individual.h

src/helpers.cpp

src/helpers.h

src/likelihood_funcs.cpp

src/likelihood_funcs.h

src/proposal.cpp

src/serosolver.dll

test_long/readme_log.txt

test_long/readme_serosolver_settings.RData

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-plotting.R tests/testthat/test-simulations.R tests/testthat/test.R

tests/testthat/test.R~

tmp.pdf

vignettes/antigenic_map.tiff

vignettes/cs1_vignette.Rmd vignettes/cs2_vignette.Rmd

vignettes/figures/guide_fig1.png

vignettes/plos.csl

vignettes/readme_log.txt

vignettes/readme_serosolver_settings.RData

vignettes/serosolver-quick_start_guide.Rmd

vignettes/vignette_references.bib

seroanalytics/serosolver documentation built on Dec. 14, 2024, 5:33 a.m.

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seroanalytics/serosolver
Inference Framework for Serological Data

Files in seroanalytics/serosolver
Inference Framework for Serological Data

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seroanalytics/serosolver Inference Framework for Serological Data

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seroanalytics/serosolver
Inference Framework for Serological Data

Files in seroanalytics/serosolver
Inference Framework for Serological Data