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 SIRtype model with wildtype and mutant strains and treatment 
simulate_fit_flu()

Fitting a SIRtype 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 SEIRtype model 
simulate_sirdemographic_ode()

Basic SIR model with births and deaths 
simulate_sirdemographic_stochastic()

Stochastic simulation of an SIRtype 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 