Files in kylieainslie/vacamole
Deterministic Age-Structured SEIR model with Vaccination

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

Meta/vignette.rds

NAMESPACE

R/age_struct_seir_ode.R R/age_struct_seir_ode2.R R/calc_waning.R R/choose_contact_matrix.R R/convert_contact_matrices.R R/convert_vac_schedule.R R/convert_vac_schedule2.R R/fit_to_data_func.R R/get_foi.R R/get_transmission_matrix.R R/helper_functions.R R/likelihood_func2.R R/my_rmultinom.R R/na_to_zero.R R/postprocess_age_struct_model_output2.R R/stochastic_age_struct_seir_ode.R R/summarise_results.R README.md

_pkgdown.yml

doc/quick_start_guide.R doc/quick_start_guide.Rmd

doc/quick_start_guide.html

docs/404.html

docs/LICENSE-text.html

docs/articles/index.html

docs/articles/model_diagram.png

docs/articles/quick_start_guide.html

docs/articles/quick_start_guide_files/header-attrs-2.11/header-attrs.js

docs/articles/quick_start_guide_files/kePrint-0.0.1/kePrint.js

docs/articles/quick_start_guide_files/lightable-0.0.1/lightable.css

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/age_struct_seir_ode.html

docs/reference/calc_ve_w_waning.html

docs/reference/choose_contact_matrix.html

docs/reference/convert_contact_matrices.html

docs/reference/convert_vac_schedule.html

docs/reference/forward_sim_func_wrap.html

docs/reference/get_foi.html

docs/reference/get_transmission_matrix.html

docs/reference/index.html

docs/reference/likelihood_func.html

docs/reference/model_run_wrapper.html

docs/reference/my_rmultinom.html

docs/reference/postprocess_age_struct_model_output.html

docs/reference/seir_ode.html

docs/reference/seir_ode_2.html

docs/reference/stochastic_age_struct_seir_ode.html

docs/reference/summarise_results.html

docs/reference/vac-a-mole-package.html

docs/reference/wide_to_long.html

docs/reference/wrangle_results.html

inst/extdata/data/case_data_upto_2021-11-28.rds

inst/extdata/data/case_data_upto_20210622.rds

inst/extdata/data/case_data_upto_2022-03-12.rds

inst/extdata/data/case_data_upto_2022-05-21.rds

inst/extdata/data/case_data_upto_2022-07-10.rds

inst/extdata/data/case_data_upto_2022-07-24.rds

inst/extdata/data/case_data_upto_2022-08-19.rds

inst/extdata/inputs/ProbabilitiesDelays_20210107.xlsx

inst/extdata/inputs/breakpoints_for_model_fit_v3.csv

inst/extdata/inputs/contact_matrices/converted/transmission_matrix_april_2017.rds

inst/extdata/inputs/contact_matrices/converted/transmission_matrix_april_2020.rds

inst/extdata/inputs/contact_matrices/converted/transmission_matrix_february_2021.rds

inst/extdata/inputs/contact_matrices/converted/transmission_matrix_june_2020.rds

inst/extdata/inputs/contact_matrices/converted/transmission_matrix_june_2021.rds

inst/extdata/inputs/contact_matrices/converted/transmission_matrix_november_2021.rds

inst/extdata/inputs/contact_matrices/converted/transmission_matrix_september_2020.rds

inst/extdata/inputs/contact_matrices/raw/mean_contactpatterns_pico1_10y.rds

inst/extdata/inputs/contact_matrices/raw/mean_contactpatterns_pico2_10y.rds

inst/extdata/inputs/contact_matrices/raw/mean_contactpatterns_pico3_10y.rds

inst/extdata/inputs/contact_matrices/raw/mean_contactpatterns_pico4_10y.rds

inst/extdata/inputs/contact_matrices/raw/mean_contactpatterns_pico5_10y.rds

inst/extdata/inputs/contact_matrices/raw/mean_contactpatterns_pienter3_10y.rds

inst/extdata/inputs/transition_rates.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_12plus.csv

inst/extdata/inputs/vaccination_schedules/vac_schedule_18plus.csv

inst/extdata/inputs/vaccination_schedules/vac_schedule_18plus_synth.xlsx

inst/extdata/inputs/vaccination_schedules/vac_schedule_5plus.csv

inst/extdata/inputs/vaccination_schedules/vac_schedule_60plus_0.5_60minus_0.2.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_60plus_0.5_60minus_0.5.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_60plus_0.8_60minus_0.2.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_60plus_0.8_60minus_0.5.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_real_20220709.csv

inst/extdata/inputs/vaccination_schedules/vac_schedule_real_20220709.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_real_w_4th_and_5th_dose.csv

inst/extdata/inputs/vaccination_schedules/vac_schedule_real_w_4th_and_5th_dose.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_real_w_booster.csv

inst/extdata/inputs/vaccination_schedules/vac_schedule_scenario_hub_round1.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_scenario_hub_round1_AC.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_scenario_hub_round1_BD.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_scenario_hub_round2_AC.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_scenario_hub_round2_BD.rds

inst/extdata/inputs/vaccination_schedules/vac_schedule_scenario_hub_round2_no_boost.rds

inst/extdata/inputs/ve_estimates/ve_dat.xlsx

inst/extdata/inputs/ve_estimates/ve_dat_round2_AB.xlsx

inst/extdata/inputs/ve_estimates/ve_dat_round2_CD.xlsx

inst/extdata/inputs/ve_estimates/ve_params.rds

inst/extdata/results/all_res_for_plot.rds

inst/extdata/results/model_fits/beta_draws.rds

inst/extdata/results/model_fits/beta_draws_2022-08-19.rds

inst/extdata/results/model_fits/initial_conditions.rds

inst/extdata/results/model_fits/initial_conditions2.rds

inst/extdata/results/model_fits/initial_conditions_2022-08-19.rds

inst/extdata/results/model_fits/manuscript/beta_draws.rds

inst/extdata/results/model_fits/manuscript/initial_conditions_manuscript.rds

inst/extdata/results/model_fits/manuscript/mle_list.rds

inst/extdata/results/model_fits/mle_list.rds

inst/extdata/results/model_fits/mle_list_2022-08-19.rds

inst/extdata/results/scenario_hub/2022-07-24-rivm-vacamole.rds

inst/extdata/results/scenario_hub/2022-07-24-rivm-vacamole_no_boost.rds

inst/extdata/results/scenario_hub/test_output.rds

vacamole.Rproj

vignettes/.gitignore

vignettes/fit_model_to_case_data.Rmd vignettes/manuscript_main_analysis.Rmd

vignettes/model_diagram.png

vignettes/parameter_description_table.xlsx

vignettes/quick_start_guide.Rmd

kylieainslie/vacamole documentation built on Oct. 15, 2024, 10:17 a.m.

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kylieainslie/vacamole
Deterministic Age-Structured SEIR model with Vaccination

Files in kylieainslie/vacamole
Deterministic Age-Structured SEIR model with Vaccination

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kylieainslie/vacamole Deterministic Age-Structured SEIR model with Vaccination

Files in kylieainslie/vacamole Deterministic Age-Structured SEIR model with Vaccination

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We want your feedback!

kylieainslie/vacamole
Deterministic Age-Structured SEIR model with Vaccination

Files in kylieainslie/vacamole
Deterministic Age-Structured SEIR model with Vaccination