├── .gitignore ├── .nojekyll ├── README.md ├── _footer.html ├── _posts ├── 2020-02-18-analysing-covid-19-2019-ncov-outbreak-data-with-r-part-1 │ ├── analysing-covid-19-2019-ncov-outbreak-data-with-r-part-1.Rmd │ └── assets │ │ ├── Hubei_Health_Commission_page.png │ │ ├── Li_et_al_fig3.png │ │ ├── SIR.png │ │ ├── example_NSW_Health_media_release.png │ │ └── provinces_confirmed_jh.rda ├── 2020-03-01-analysing-covid-19-2019-ncov-outbreak-data-with-r-part-2 │ └── analysing-covid-19-2019-ncov-outbreak-data-with-r-part-2.Rmd ├── 2020-03-06-covid-19-call-to-arms │ ├── assets │ │ ├── Cori_empirical_si_model_fit_hubei_daily-1.png │ │ └── Delacroix.jpg │ └── covid-19-call-to-arms.Rmd ├── 2020-03-10-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-1 │ ├── churches2020modellingcovid19rpart1_references.bib │ └── modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-1.Rmd ├── 2020-03-18-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-2 │ ├── _icm.control.seiqhr.R │ ├── _icm.control.seiqhrf.R │ ├── _icm.control.seir.R │ ├── _icm.icm.seiqhrf.R │ ├── _icm.mod.init.seiqhr.R │ ├── _icm.mod.init.seiqhrf.R │ ├── _icm.mod.init.seir.R │ ├── _icm.mod.status.seiqhr.R │ ├── _icm.mod.status.seiqhrf.R │ ├── _icm.mod.status.seir.R │ ├── _icm.mod.vital.seiqhr.R │ ├── _icm.mod.vital.seiqhrf.R │ ├── _icm.mod.vital.seir.R │ ├── _icm.saveout.seiqhrf.R │ ├── _icm.utils.seiqhr.R │ ├── _icm.utils.seiqhrf.R │ ├── _icm.utils.seir.R │ ├── _model.R │ ├── _modelling_misc.R │ ├── _module-fx.R │ ├── churches2020modellingcovid19rpart2_references.bib │ └── modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-2.Rmd ├── 2020-03-20-covid-19-trends-and-trajectories │ ├── covid-19-trends-and-trajectories.Rmd │ └── distill-preview.png └── 2020-03-20-dont-speculate-simulate │ └── dont-speculate-simulate.Rmd ├── _site.yml ├── _subscribe.html ├── about.Rmd ├── assets ├── Hubei_Health_Commission_page.png ├── Li_et_al_fig3.png ├── SIR.png ├── TimC.jpg ├── example_NSW_Health_media_release.png └── provinces_confirmed_jh.rda ├── blog.Rproj ├── docs ├── about.html ├── assets │ ├── Hubei_Health_Commission_page.png │ ├── Li_et_al_fig3.png │ ├── SIR.png │ ├── TimC.jpg │ ├── example_NSW_Health_media_release.png │ └── provinces_confirmed_jh.rda ├── index.html ├── index.xml ├── posts │ ├── 2020-02-18-analysing-covid-19-2019-ncov-outbreak-data-with-r-part-1 │ │ ├── analysing-covid-19-2019-ncov-outbreak-data-with-r-part-1_files │ │ │ └── figure-html5 │ │ │ │ ├── Cori_empirical_si_model_fit_hubei_daily-1.png │ │ │ │ ├── Cori_model_get_data_not_hubei-1.png │ │ │ │ ├── Cori_model_get_data_wuhan-1.png │ │ │ │ ├── Cori_parametric_si_model_fit2_hubei-1.png │ │ │ │ ├── Cori_parametric_si_model_fit_hubei-1.png │ │ │ │ ├── Cori_uncertain_si_model_fit_hubei-1.png │ │ │ │ ├── Cori_uncertain_si_model_fit_hubei_daily-1.png │ │ │ │ ├── JHU_incidence-1.png │ │ │ │ ├── SIR_model_plot_extrapolated-1.png │ │ │ │ ├── SIR_model_plot_fitted_data-1.png │ │ │ │ ├── SIR_model_plot_no_intervention-1.png │ │ │ │ ├── SIR_model_plot_no_intervention_ascertainment_adjustment-1.png │ │ │ │ ├── SIR_model_plot_no_intervention_log-1.png │ │ │ │ ├── all_provinces_cum_incidence-1.png │ │ │ │ ├── all_provinces_incidence-1.png │ │ │ │ ├── cumulative_deaths-1.png │ │ │ │ ├── cumulative_incidence-1.png │ │ │ │ ├── daily_case_deaths_plot-1.png │ │ │ │ ├── daily_deaths_plot-1.png │ │ │ │ ├── daily_incidence-1.png │ │ │ │ ├── est_R0_decay-1.png │ │ │ │ ├── est_R0_growth-1.png │ │ │ │ ├── fit_incidence_object-1.png │ │ │ │ ├── hubei_daily_incidence_adj-1.png │ │ │ │ ├── log_cumulative_incidence-1.png │ │ │ │ ├── nsw_graph-1.png │ │ │ │ ├── plot_incidence_object-1.png │ │ │ │ ├── test_projection_Hubei_decay-1.png │ │ │ │ └── test_projection_Hubei_growth-1.png │ │ ├── assets │ │ │ ├── Hubei_Health_Commission_page.png │ │ │ ├── Li_et_al_fig3.png │ │ │ ├── SIR.png │ │ │ ├── example_NSW_Health_media_release.png │ │ │ └── provinces_confirmed_jh.rda │ │ └── index.html │ ├── 2020-03-01-analysing-covid-19-2019-ncov-outbreak-data-with-r-part-2 │ │ ├── analysing-covid-19-2019-ncov-outbreak-data-with-r-part-2_files │ │ │ └── figure-html5 │ │ │ │ ├── all_provinces_incidence_different_scales_separate_prisons-1.png │ │ │ │ ├── get_iran_data-1.png │ │ │ │ ├── get_italy_data-1.png │ │ │ │ ├── get_japan_data-1.png │ │ │ │ ├── get_korea_data-1.png │ │ │ │ ├── hubei_incidence_separate_prisons-1.png │ │ │ │ ├── incidence_object_all_data_fit-1.png │ │ │ │ ├── incidence_object_all_data_refit-1.png │ │ │ │ ├── incidence_object_all_data_refit_predict-1.png │ │ │ │ ├── incidence_object_all_data_refit_predict_tail-1.png │ │ │ │ ├── incidence_object_refit-1.png │ │ │ │ ├── incidence_object_refit_predict-1.png │ │ │ │ ├── unnamed-chunk-1-1.png │ │ │ │ ├── unnamed-chunk-10-1.png │ │ │ │ ├── unnamed-chunk-11-1.png │ │ │ │ ├── unnamed-chunk-12-1.png │ │ │ │ ├── unnamed-chunk-13-1.png │ │ │ │ ├── unnamed-chunk-14-1.png │ │ │ │ ├── unnamed-chunk-15-1.png │ │ │ │ ├── unnamed-chunk-16-1.png │ │ │ │ ├── unnamed-chunk-17-1.png │ │ │ │ ├── unnamed-chunk-18-1.png │ │ │ │ ├── unnamed-chunk-19-1.png │ │ │ │ ├── unnamed-chunk-2-1.png │ │ │ │ ├── unnamed-chunk-20-1.png │ │ │ │ ├── unnamed-chunk-21-1.png │ │ │ │ ├── unnamed-chunk-22-1.png │ │ │ │ ├── unnamed-chunk-23-1.png │ │ │ │ ├── unnamed-chunk-24-1.png │ │ │ │ ├── unnamed-chunk-25-1.png │ │ │ │ ├── unnamed-chunk-26-1.png │ │ │ │ ├── unnamed-chunk-27-1.png │ │ │ │ ├── unnamed-chunk-28-1.png │ │ │ │ ├── unnamed-chunk-29-1.png │ │ │ │ ├── unnamed-chunk-30-1.png │ │ │ │ ├── unnamed-chunk-31-1.png │ │ │ │ ├── unnamed-chunk-32-1.png │ │ │ │ ├── unnamed-chunk-33-1.png │ │ │ │ ├── unnamed-chunk-34-1.png │ │ │ │ ├── unnamed-chunk-35-1.png │ │ │ │ ├── unnamed-chunk-36-1.png │ │ │ │ ├── unnamed-chunk-37-1.png │ │ │ │ ├── unnamed-chunk-38-1.png │ │ │ │ ├── unnamed-chunk-39-1.png │ │ │ │ ├── unnamed-chunk-40-1.png │ │ │ │ ├── unnamed-chunk-41-1.png │ │ │ │ ├── unnamed-chunk-42-1.png │ │ │ │ ├── unnamed-chunk-43-1.png │ │ │ │ ├── unnamed-chunk-44-1.png │ │ │ │ ├── unnamed-chunk-45-1.png │ │ │ │ ├── unnamed-chunk-46-1.png │ │ │ │ ├── unnamed-chunk-47-1.png │ │ │ │ ├── unnamed-chunk-48-1.png │ │ │ │ ├── unnamed-chunk-49-1.png │ │ │ │ ├── unnamed-chunk-5-1.png │ │ │ │ ├── unnamed-chunk-50-1.png │ │ │ │ ├── unnamed-chunk-51-1.png │ │ │ │ ├── unnamed-chunk-52-1.png │ │ │ │ ├── unnamed-chunk-53-1.png │ │ │ │ ├── unnamed-chunk-54-1.png │ │ │ │ ├── unnamed-chunk-55-1.png │ │ │ │ ├── unnamed-chunk-56-1.png │ │ │ │ ├── unnamed-chunk-57-1.png │ │ │ │ ├── unnamed-chunk-58-1.png │ │ │ │ ├── unnamed-chunk-6-1.png │ │ │ │ ├── unnamed-chunk-7-1.png │ │ │ │ ├── unnamed-chunk-8-1.png │ │ │ │ └── unnamed-chunk-9-1.png │ │ └── index.html │ ├── 2020-03-06-covid-19-call-to-arms │ │ ├── assets │ │ │ ├── Cori_empirical_si_model_fit_hubei_daily-1.png │ │ │ └── Delacroix.jpg │ │ └── index.html │ ├── 2020-03-10-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-1 │ │ ├── churches2020modellingcovid19rpart1_references.bib │ │ ├── index.html │ │ └── modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-1_files │ │ │ └── figure-html5 │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-1-2.png │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── 2020-03-18-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-2 │ │ ├── churches2020modellingcovid19rpart2_references.bib │ │ ├── index.html │ │ └── modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-2_files │ │ │ ├── figure-html5 │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-11-2.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-12-2.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ │ └── kePrint-0.0.1 │ │ │ └── kePrint.js │ ├── 2020-03-20-dont-speculate-simulate │ │ └── index.html │ └── posts.json ├── site_libs │ ├── DiagrammeR-styles-0.2 │ │ └── styles.css │ ├── bowser-1.9.3 │ │ └── bowser.min.js │ ├── distill-2.2.21 │ │ └── template.v2.js │ ├── font-awesome-5.1.0 │ │ ├── css │ │ │ ├── all.css │ │ │ └── v4-shims.css │ │ └── webfonts │ │ │ ├── fa-brands-400.eot │ │ │ ├── fa-brands-400.svg │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.eot │ │ │ ├── fa-regular-400.svg │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.eot │ │ │ ├── fa-solid-900.svg │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff │ │ │ └── fa-solid-900.woff2 │ ├── grViz-binding-1.0.1 │ │ └── grViz.js │ ├── 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