├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── test-coverage.yaml ├── .gitignore ├── .nojekyll ├── CRAN-RELEASE ├── DESCRIPTION ├── DSAIDE.Rproj ├── Meta └── vignette.rds ├── NAMESPACE ├── NEWS.md ├── R ├── DSAIDE-package.R ├── data.R ├── dsaidemenu.R ├── generate_documentation.R ├── generate_fctcall.R ├── generate_ggplot.R ├── generate_plotly.R ├── generate_shinyinput.R ├── generate_text.R ├── run_model.R ├── simulate_Characteristics_of_ID_ode.R ├── simulate_Complex_ID_Control_ode.R ├── simulate_Drug_Resistance_Evolution_stochastic.R ├── simulate_Environmental_Transmission_model_ode.R ├── simulate_Host_Heterogeneity_Model_ode.R ├── simulate_SEIRSd_model_stochastic.R ├── simulate_SIRSd_model_ode.R ├── simulate_SIRSd_model_stochastic.R ├── simulate_SIR_model_discrete.R ├── simulate_SIR_model_ode.R ├── simulate_SIR_modelexploration.R ├── simulate_SIR_usanalysis.R ├── simulate_Vector_transmission_model_ode.R ├── simulate_directtransmission_ode.R ├── simulate_flu_fit.R ├── simulate_idcontrolmultigroup_ode.R ├── simulate_idcontrolmultioutbreak_ode.R ├── simulate_idpatterns_ode.R ├── simulate_idsurveillance_ode.R ├── simulate_idvaccine_ode.R ├── simulate_multipathogen_ode.R └── simulate_noro_fit.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── auxiliary ├── DSAIDE.R ├── analytical_SS_calculations │ ├── SEIR_steadystate.nb │ ├── SIRd_steadystate.nb │ ├── SS-SEIR-waning-immunity.wxm │ ├── SS-birth-death.wxm │ └── SS-waning-immunity.wxm ├── docsfordevelopers │ ├── Alexis Vittengl - DSAIDE notes BKM.docx │ ├── BIOL4195_DiseaseEcology_Syllabus_20200124.pdf │ ├── ID Epi Course List.xlsx │ ├── documentation.md │ ├── notes-and-to-do.md │ └── package-stats.R ├── dsaide-logo.png ├── dsaide-logo.svg ├── extdata │ ├── flu1918data.csv │ ├── flu1918data.xlsx │ └── norodata.csv ├── helperfunctions │ ├── get_settings.R │ ├── processing_script.R │ └── write_tasktext.R ├── oldfiles │ ├── dsaide_references_old.bib │ ├── evolutionarydynamics_documentation.Rmd │ ├── evolutionarydynamics_settings.R │ ├── fill_tasktable.R │ ├── generate_shinyinput-with-doc-parsing.R │ ├── generatemodeltable.R │ ├── hostheterogeneity_documentation.Rmd │ ├── hostheterogeneity_settings.R │ ├── idcontrolcomplex_documentation.Rmd │ ├── idcontrolcomplex_settings.R │ ├── idcontrolmultigroup_documentation.Rmd │ ├── idcontrolmultigroup_settings.R │ ├── idcontrolmultioutbreak_documentation.Rmd │ ├── idcontrolmultioutbreak_settings.R │ ├── idcontrolvaccine_documentation.Rmd │ ├── idcontrolvaccine_settings.R │ ├── maternalimmunity_documentation.Rmd │ ├── maternalimmunity_settings.R │ ├── modelexploration_documentation.Rmd │ ├── modelexploration_settings.R │ ├── multipathogen_documentation.Rmd │ ├── multipathogen_settings.R │ ├── parasitemodel_documentation.Rmd │ ├── parasitemodel_settings.R │ ├── reproductivenumber1_documentation.Rmd │ ├── reproductivenumber1_settings.R │ ├── reproductivenumber2_documentation.Rmd │ ├── reproductivenumber2_settings.R │ ├── run_model.R │ ├── simulate_environmentaltransmission_ode.R │ ├── simulate_evolution_stochastic.R │ ├── simulate_fit_norovirus.r │ ├── simulate_hostheterogeneity_ode.R │ ├── simulate_idcharacteristics_ode.R │ ├── simulate_idcontrol_ode.R │ ├── simulate_reproductivenumber1_ode.R │ ├── simulate_reproductivenumber2_ode.R │ ├── simulate_schoolclosure_ode.R │ ├── simulate_seir_stochastic.R │ ├── simulate_sir_discrete.R │ ├── simulate_sir_ode.R │ ├── simulate_sirdemographic_ode.R │ └── simulate_sirdemographic_stochastic.R └── toimplement_code_apps │ ├── DESCRIPTION_with_additional_app_authors │ ├── covidstochastic_documentation.Rmd │ ├── covidstochastic_settings.R │ ├── diagrammeR-code.R │ ├── download_code.R │ ├── generate_equations.R │ ├── globalwarming_Answers.Rmd │ ├── globalwarming_documentation.Rmd │ ├── globalwarming_documentation.html │ ├── globalwarming_settings.R │ ├── idsurveillance_documentation.Rmd │ ├── maternalimmunity_documentation.Rmd │ ├── parasitemodel_documentation.Rmd │ ├── simulate_covid_stochastic.R │ ├── simulate_globalwarming_ode.R │ ├── simulate_maternalimmunity_ode.R │ └── simulate_parasites_ode.R ├── codecov.yml ├── cran-comments.md ├── data ├── flu1918data.rda └── norodata.rda ├── doc ├── DSAIDE.R ├── DSAIDE.Rmd └── DSAIDE.html ├── docs ├── 404.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── DSAIDE.html │ ├── DSAIDE_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── appexample.png │ ├── index.html │ ├── mainmenu.png │ ├── modelexample.png │ └── whattodoexample.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── extra.css ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── link.svg ├── logo.png ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── DSAIDE-package.html │ ├── Rplot001.png │ ├── dsaidemenu.html │ ├── figures │ │ └── logo.png │ ├── flu1918data.html │ ├── generate_documentation.html │ ├── generate_fctcall.html │ ├── generate_ggplot.html │ ├── generate_plotly.html │ ├── generate_shinyinput.html │ ├── generate_text.html │ ├── index.html │ ├── norodata.html │ ├── run_model.html │ ├── simulate_Characteristics_of_ID_ode-1.png │ ├── simulate_Characteristics_of_ID_ode.html │ ├── simulate_Complex_ID_Control_ode-1.png │ ├── simulate_Complex_ID_Control_ode.html │ ├── simulate_Drug_Resistance_Evolution_stochastic-1.png │ ├── simulate_Drug_Resistance_Evolution_stochastic.html │ ├── simulate_Environmental_Transmission_model_ode-1.png │ ├── simulate_Environmental_Transmission_model_ode.html │ ├── simulate_Host_Heterogeneity_Model_ode-1.png │ ├── simulate_Host_Heterogeneity_Model_ode.html │ ├── simulate_SEIRSd_model_stochastic-1.png │ ├── simulate_SEIRSd_model_stochastic.html │ ├── simulate_SIRSd_model_ode-1.png │ ├── simulate_SIRSd_model_ode.html │ ├── simulate_SIRSd_model_stochastic-1.png │ ├── simulate_SIRSd_model_stochastic.html │ ├── simulate_SIR_model_discrete-1.png │ ├── simulate_SIR_model_discrete.html │ ├── simulate_SIR_model_ode-1.png │ ├── simulate_SIR_model_ode.html │ ├── simulate_SIR_modelexploration-1.png │ ├── simulate_SIR_modelexploration.html │ ├── simulate_SIR_usanalysis-1.png │ ├── simulate_SIR_usanalysis.html │ ├── simulate_Vector_transmission_model_ode-1.png │ ├── simulate_Vector_transmission_model_ode.html │ ├── simulate_directtransmission_ode-1.png │ ├── simulate_directtransmission_ode.html │ ├── simulate_flu_fit.html │ ├── simulate_idcontrolmultigroup_ode.html │ ├── simulate_idcontrolmultioutbreak_ode-1.png │ ├── simulate_idcontrolmultioutbreak_ode.html │ ├── simulate_idpatterns_ode-1.png │ ├── simulate_idpatterns_ode.html │ ├── simulate_idsurveillance_ode-1.png │ ├── simulate_idsurveillance_ode.html │ ├── simulate_idvaccine_ode-1.png │ ├── simulate_idvaccine_ode.html │ ├── simulate_multipathogen_ode-1.png │ ├── simulate_multipathogen_ode.html │ └── simulate_noro_fit.html └── sitemap.xml ├── inst ├── CITATION ├── DSAIDE │ ├── app.R │ ├── google-analytics.html │ ├── packagestyle.css │ └── rsconnect │ │ └── shinyapps.io │ │ ├── epibiouga │ │ └── dsaide.dcf │ │ └── handelgroup │ │ └── dsaide.dcf ├── appinformation │ ├── apptable.tsv │ ├── basicsir_documentation.Rmd │ ├── basicsir_documentation.html │ ├── basicsir_tasktable.tsv │ ├── directtransmission_documentation.Rmd │ ├── directtransmission_documentation.html │ ├── directtransmission_tasktable.tsv │ ├── dsaide_references.bib │ ├── environmentaltransmission_documentation.Rmd │ ├── environmentaltransmission_documentation.html │ ├── environmentaltransmission_tasktable.tsv │ ├── evolution_documentation.Rmd │ ├── evolution_documentation.html │ ├── evolution_tasktable.tsv │ ├── fitflu_documentation.Rmd │ ├── fitflu_documentation.html │ ├── fitflu_tasktable.tsv │ ├── fitnoro_documentation.Rmd │ ├── fitnoro_documentation.html │ ├── fitnoro_tasktable.tsv │ ├── hostheterogeneity_documentation.Rmd │ ├── hostheterogeneity_documentation.html │ ├── hostheterogeneity_tasktable.tsv │ ├── idcharacteristics_documentation.Rmd │ ├── idcharacteristics_documentation.html │ ├── idcharacteristics_tasktable.tsv │ ├── idcontrolcomplex_documentation.Rmd │ ├── idcontrolcomplex_documentation.html │ ├── idcontrolcomplex_tasktable.tsv │ ├── idcontrolmultigroup_documentation.Rmd │ ├── idcontrolmultigroup_documentation.html │ ├── idcontrolmultigroup_tasktable.tsv │ ├── idcontrolmultioutbreak_documentation.Rmd │ ├── idcontrolmultioutbreak_documentation.html │ ├── idcontrolmultioutbreak_tasktable.tsv │ ├── idcontrolvaccine_documentation.Rmd │ ├── idcontrolvaccine_documentation.html │ ├── idcontrolvaccine_tasktable.tsv │ ├── idpatterns_documentation.Rmd │ ├── idpatterns_documentation.html │ ├── idpatterns_tasktable.tsv │ ├── idsurveillance_documentation.Rmd │ ├── idsurveillance_documentation.html │ ├── idsurveillance_tasktable.tsv │ ├── modelexploration_documentation.Rmd │ ├── modelexploration_documentation.html │ ├── modelexploration_tasktable.tsv │ ├── multipathogen_documentation.Rmd │ ├── multipathogen_documentation.html │ ├── multipathogen_tasktable.tsv │ ├── reproductivenumber1_documentation.Rmd │ ├── reproductivenumber1_documentation.html │ ├── reproductivenumber1_tasktable.tsv │ ├── reproductivenumber2_documentation.Rmd │ ├── reproductivenumber2_documentation.html │ ├── reproductivenumber2_tasktable.tsv │ ├── startup_script.R │ ├── stochasticseir_documentation.Rmd │ ├── stochasticseir_documentation.html │ ├── stochasticseir_tasktable.tsv │ ├── stochasticsir_documentation.Rmd │ ├── stochasticsir_documentation.html │ ├── stochasticsir_tasktable.tsv │ ├── usanalysis_documentation.Rmd │ ├── usanalysis_documentation.html │ ├── usanalysis_tasktable.tsv │ ├── vectortransmission_documentation.Rmd │ ├── vectortransmission_documentation.html │ └── vectortransmission_tasktable.tsv ├── media │ ├── SIRSd_model_figure.png │ ├── SIRSd_model_figure.svg │ ├── basicsir_figure.png │ ├── basicsir_figure.svg │ ├── directtransmission_figure.png │ ├── directtransmission_figure.svg │ ├── environmentaltransmission_figure.png │ ├── environmentaltransmission_figure.svg │ ├── evolutionarydynamics_figure.png │ ├── evolutionarydynamics_figure.svg │ ├── fitflu_figure.png │ ├── fitflu_figure.svg │ ├── fitnoro_figure.png │ ├── fitnoro_figure.svg │ ├── hostheterogeneity_figure.png │ ├── hostheterogeneity_figure.svg │ ├── idcharacteristics_figure.png │ ├── idcharacteristics_figure.svg │ ├── idcontrolcomplex_figure.png │ ├── idcontrolcomplex_figure.svg │ ├── idcontrolmultigroup_figure.png │ ├── idcontrolmultigroup_figure.svg │ ├── idcontrolmultioutbreak_figure.png │ ├── idcontrolmultioutbreak_figure.svg │ ├── idpatterns_figure.png │ ├── idpatterns_figure.svg │ ├── idsurveillance_figure.png │ ├── maternalimmunity_figure.png │ ├── maternalimmunity_figure.svg │ ├── multipathogen_figure.png │ ├── multipathogen_figure.svg │ ├── parasitemodel_figure.png │ ├── stochasticseir_figure.png │ ├── stochasticseir_figure.svg │ ├── vectortransmission_figure.png │ └── vectortransmission_figure.svg └── simulatorfunctions │ ├── simulate_Characteristics_of_ID_ode.R │ ├── simulate_Complex_ID_Control_ode.R │ ├── simulate_Drug_Resistance_Evolution_stochastic.R │ ├── simulate_Environmental_Transmission_model_ode.R │ ├── simulate_Host_Heterogeneity_Model_ode.R │ ├── simulate_SEIRSd_model_stochastic.R │ ├── simulate_SIRSd_model_ode.R │ ├── simulate_SIRSd_model_stochastic.R │ ├── simulate_SIR_model_discrete.R │ ├── simulate_SIR_model_ode.R │ ├── simulate_SIR_modelexploration.R │ ├── simulate_SIR_usanalysis.R │ ├── simulate_Vector_transmission_model_ode.R │ ├── simulate_directtransmission_ode.R │ ├── simulate_flu_fit.R │ ├── simulate_idcontrolmultigroup_ode.R │ ├── simulate_idcontrolmultioutbreak_ode.R │ ├── simulate_idpatterns_ode.R │ ├── simulate_idsurveillance_ode.R │ ├── simulate_idvaccine_ode.R │ ├── simulate_multipathogen_ode.R │ ├── simulate_noro_fit.R │ └── simulatorfunctions.zip ├── man ├── DSAIDE-package.Rd ├── dsaidemenu.Rd ├── figures │ └── logo.png ├── flu1918data.Rd ├── generate_documentation.Rd ├── generate_fctcall.Rd ├── generate_ggplot.Rd ├── generate_plotly.Rd ├── generate_shinyinput.Rd ├── generate_text.Rd ├── norodata.Rd ├── run_model.Rd ├── simulate_Characteristics_of_ID_ode.Rd ├── simulate_Complex_ID_Control_ode.Rd ├── simulate_Drug_Resistance_Evolution_stochastic.Rd ├── simulate_Environmental_Transmission_model_ode.Rd ├── simulate_Host_Heterogeneity_Model_ode.Rd ├── simulate_SEIRSd_model_stochastic.Rd ├── simulate_SIRSd_model_ode.Rd ├── simulate_SIRSd_model_stochastic.Rd ├── simulate_SIR_model_discrete.Rd ├── simulate_SIR_model_ode.Rd ├── simulate_SIR_modelexploration.Rd ├── simulate_SIR_usanalysis.Rd ├── simulate_Vector_transmission_model_ode.Rd ├── simulate_directtransmission_ode.Rd ├── simulate_flu_fit.Rd ├── simulate_idcontrolmultigroup_ode.Rd ├── simulate_idcontrolmultioutbreak_ode.Rd ├── simulate_idpatterns_ode.Rd ├── simulate_idsurveillance_ode.Rd ├── simulate_idvaccine_ode.Rd ├── simulate_multipathogen_ode.Rd └── simulate_noro_fit.Rd ├── pkgdown ├── extra.css └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── testthat.R └── testthat │ ├── Rplots.pdf │ ├── SIR_model.Rds │ ├── test-all_simulators.R │ ├── test-fit-apps.R │ ├── test-generate_documentation.R │ ├── test-generate_ggplot.R │ ├── test-generate_plotly.R │ ├── test-generate_shinyinput.R │ ├── test-generate_text.R │ ├── test-generate_usplot.R │ ├── 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