# Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)

## Documentation for package ‘DSAIDE’ version 0.8.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

DSAIDE | DSAIDE: A package to learn about Dynamical Systems Approaches to Infectious Disease Epidemiology
dsaidemenu | The main menu for the DSAIDE package
flu1918data | 1918 Influenza mortality data
generate_documentation | A helper function which processes and displays the documentation part for each app
generate_fctcall | A helper function that produces a call to a simulator function for specific settings
generate_ggplot | A helper function that takes simulation results and produces ggplot plots
generate_plotly | A helper function that takes simulation results and produces plotly plots
generate_shinyinput | A helper function that takes a model and generates shiny UI elements
generate_text | A helper function that takes result from the simulators and produces text output
norodata | Cases of norovirus during an outbreak
run_model | A function that runs an app for specific settings and processes results for plot and text generation
simulate_directtransmission_ode | Simulation of a compartmental infectious disease transmission model illustrating different types of direct transmission
simulate_environmentaltransmission_ode | Environmental Transmission model
simulate_evolution_stochastic | Stochastic simulation of a compartmental SIR-type model with wild-type and mutant strains and treatment
simulate_fit_flu | Fitting a SIR-type model to flu data
simulate_fit_noro | Fitting a simple SIR type model to norovirus outbreak data
simulate_heterogeneity_ode | Simulation of a compartmental infectious disease transmission model with 2 types of hosts
simulate_idcharacteristics_ode | Simulation of an infectious disease transmission model with multiple compartments
simulate_idcontrolmultioutbreak_ode | Simulation of a compartmental infectious disease transmission model to study the reproductive number
simulate_idcontrol_ode | Simulation of a compartmental infectious disease transmission model including different control mechanisms
simulate_idpatterns_ode | Simulation of a compartmental infectious disease transmission model including seasonality
simulate_idsurveillance_ode | Simulation of a compartmental infectious disease transmission model illustrating the impact of ID surveillance
simulate_maternalimmunity_ode | Simulation of a MSEIR model that represents a group of the population that is protected by disease through maternal antibodies
simulate_modelexploration_sir | Simulation to illustrate parameter scan of the basic SIR model with births and deaths #'
simulate_multipathogen_ode | Simulation of a compartmental infectious disease transmission model with 2 types of pathogens
simulate_parasites_ode | Simulation of a compartmental infectious disease transmission model illustrating parasite infection dynamics with intermediate hosts
simulate_reproductivenumber1_ode | Basic SIR model
simulate_reproductivenumber2_ode | Simulation of a compartmental infectious disease transmission model to study the reproductive number
simulate_seir_stochastic | Stochastic simulation of an SEIR-type model
simulate_sirdemographic_ode | Basic SIR model with births and deaths
simulate_sirdemographic_stochastic | Stochastic simulation of an SIR-type model with births and deaths
simulate_sir_discrete | Basic discrete time SIR model
simulate_sir_ode | Basic SIR model
simulate_usanalysis_sir | Simulation to illustrate uncertainty and sensitivity analysis
simulate_vectortransmission_ode | Vector transmission model