Files in jameshay218/virosolver

Infer epidemic dynamics using viral load data

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE.md

NAMESPACE

R/RcppExports.R R/create_posterior_func.R R/data.R R/incidence_functions.R R/likelihoods.R R/maths_functions.R R/mcmc_help.R R/plots.R R/simulate_epidemics.R R/simulation_functions.R R/viral_load_functions.R R/zzz.R README.Rmd README.md

_config.yml

data/example_ct_data.RData

data/example_epi_data.RData

data/example_gp_partab.RData

data/example_seir_incidence.RData

data/example_seir_partab.RData

data/vignette_data1.RData

data/vignette_data2.RData

docs/404.html

docs/LICENSE.html

docs/articles/index.html

docs/articles/vignette.html

docs/articles/vignette_files/accessible-code-block-0.0.1/empty-anchor.js

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docs/articles/vignette_files/header-attrs-2.3/header-attrs.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/example_ct_data.html

docs/reference/example_gp_partab.html

docs/reference/example_seir_incidence.html

docs/reference/example_seir_partab.html

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docs/reference/index.html

docs/reference/likelihood_detectable.html

docs/reference/p_a.html

docs/reference/plot_distribution_fits.html

docs/reference/plot_posterior_density.html

docs/reference/plot_prob_infection.html

docs/reference/predicted_distribution_fits.html

docs/reference/prop_detectable_single.html

docs/reference/reverse_gp_model.html

docs/reference/simulate_observations_wrapper.html

docs/reference/simulate_reporting.html

docs/reference/simulate_viral_loads_wrapper.html

docs/sitemap.xml

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inst/doc/vignette.Rmd

inst/doc/vignette.html

inst/extdata/simulate_data.R man/SEEIRRModel.Rd man/calculate_gr_ct_relationships.Rd man/calculate_gr_ct_relationships_R0s.Rd man/compare_tsi_dist_at_gr.Rd man/create_post_func_seeirr.Rd man/create_post_func_seeirr_combined.Rd man/create_posterior_func.Rd man/create_posterior_func_detectable.Rd man/detectable_SEEIRRModel.Rd man/detectable_SEIRModel.Rd man/example_ct_data.Rd man/example_epi_data.Rd man/example_gp_partab.Rd man/example_seir_incidence.Rd man/example_seir_partab.Rd man/exponential_growth_model.Rd

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man/gaussian_process_model.Rd man/generate_viable_start_pars.Rd man/likelihood_R.Rd man/likelihood_cpp_wrapper.Rd man/likelihood_detectable.Rd man/likelihood_pos_R.Rd man/p_a.Rd man/plot_distribution_fits.Rd man/plot_posterior_density.Rd man/plot_prob_infection.Rd man/pred_dist_wrapper.Rd man/predicted_distribution_fits.Rd man/prob_detectable_curve.Rd man/prop_detectable.Rd man/prop_detectable_single.Rd man/reverse_gp_model.Rd man/simulate_detectable_wrapper.Rd man/simulate_infection_times.Rd man/simulate_observations_wrapper.Rd man/simulate_reporting.Rd man/simulate_seir_process.Rd man/simulate_seir_wrapper.Rd man/simulate_viral_loads.Rd man/simulate_viral_loads_example.Rd man/simulate_viral_loads_example_symptoms.Rd man/simulate_viral_loads_wrapper.Rd man/solveSEEIRRModel_rlsoda.Rd man/solveSEEIRRModel_rlsoda_wrapper.Rd man/solveSEIRModel_lsoda.Rd man/solveSEIRModel_lsoda_wrapper.Rd man/solveSEIRModel_rlsoda.Rd man/solveSEIRModel_rlsoda_wrapper.Rd man/solveSEIRswitch_rlsoda.Rd man/solveSEIRswitch_rlsoda_wrapper.Rd man/vignette_data1.Rd man/vignette_data2.Rd man/viral_load_func.Rd shiny_app_code/README.md shiny_app_code/UI.R shiny_app_code/global.R shiny_app_code/helpers/file_management.R shiny_app_code/helpers/helpers.R shiny_app_code/helpers/mcmc_helpers.r shiny_app_code/helpers/plots.R shiny_app_code/helpers/vk_helpers.R shiny_app_code/panels/data_visualization.R shiny_app_code/panels/mcmc_params.R shiny_app_code/panels/overview.R shiny_app_code/panels/primary_output.R shiny_app_code/panels/run_model.R shiny_app_code/panels/viral_kinetics.R shiny_app_code/server.R shiny_app_code/test_app.R

shiny_app_code/www/slide_styling.css

src/RcppExports.cpp

src/SEEIRR_model_rlsoda.c

src/SEIR_model_lsoda.c

src/SEIR_model_rlsoda.c

src/SEIR_switch_rlsoda.c

src/SIR_model_lsoda.c

src/likelihoods_cpp.cpp

src/viral_load_funcs.cpp

src/zzz.c

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vignettes/vignette.Rmd

jameshay218/virosolver documentation built on April 17, 2025, 2:57 p.m.