## All functions

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