# Dynamical Systems Approach to Infectious Disease Epidemiology

## Documentation for package ‘DSAIDE’ version 0.8.0

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

## Help Pages

DSAIDE-package | DSAIDE: A package to learn about Dynamical Systems Approaches to Infectious Disease Epidemiology
DSAIDE | DSAIDE: A package to learn about Dynamical Systems Approaches to Infectious Disease Epidemiology
dsaidemenu | The main menu for the DSAIDE package
generate_documentation | A helper function for the UI part of the Shiny apps
generate_fctcall | A function that produces a call to a simulator functions for specific settings
generate_ggplot | A helper function that takes result from the simulators and produces plots
generate_plotly | A helper function that takes result from the simulators and produces plots
generate_shinyinput | A helper function that takes a model and generates the shiny UI elements for the analyze tab
generate_text | A helper function that takes result from the simulators and produces text output
run_model | A function that runs a DSAIRM/DSAIDE app
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_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_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_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_reproductivenumber_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