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DSAIDE (version 0.8.2)

Dynamical Systems Approach to Infectious Disease Epidemiology

Description

A collection of 'shiny' apps that allow for the simulation and exploration of various infectious disease transmission dynamics scenarios. The purpose of the package is to help individuals learn about infectious disease epidemiology from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.

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Version

Install

install.packages('DSAIDE')

Monthly Downloads

372

Version

0.8.2

License

GPL-3

Issues

0

Pull Requests

0

Stars

26

Forks

18

Maintainer

Andreas Handel

Last Published

July 4th, 2019

Functions in DSAIDE (0.8.2)

generate_ggplot

A helper function that takes result from the simulators and produces plots
generate_documentation

A helper function for the UI part of the Shiny apps
dsaidemenu

The main menu for the DSAIDE package
norodata

Cases of norovirus during an outbreak
generate_fctcall

A helper function that produces a call to a simulator function for specific settings
flu1918data

1918 Influenza mortality data
generate_text

A helper function that takes result from the simulators and produces text output
generate_plotly

A helper function that takes result from the simulators and produces plots
DSAIDE

DSAIDE: A package to learn about Dynamical Systems Approaches to Infectious Disease Epidemiology
generate_shinyinput

A helper function that takes a model and generates shiny UI elements
simulate_fit_flu

Fitting a SIR-type model to flu data
simulate_seir_stochastic

Stochastic simulation of an SEIR-type model
simulate_fit_noro

Fitting a simple SIR type model to norovirus outbreak data
simulate_sir_discrete

Basic discrete time SIR model
simulate_idcontrolmultioutbreak_ode

Simulation of a compartmental infectious disease transmission model to study the reproductive number
simulate_parasites_ode

Simulation of a compartmental infectious disease transmission model illustrating parasite infection dynamics with intermediate hosts
simulate_idcontrol_ode

Simulation of a compartmental infectious disease transmission model including different control mechanisms
simulate_multipathogen_ode

Simulation of a compartmental infectious disease transmission model with 2 types of pathogens
simulate_idpatterns_ode

Simulation of a compartmental infectious disease transmission model including seasonality
simulate_idcharacteristics_ode

Simulation of an infectious disease transmission model with multiple compartments
simulate_heterogeneity_ode

Simulation of a compartmental infectious disease transmission model with 2 types of hosts
simulate_environmentaltransmission_ode

Environmental Transmission model
simulate_idsurveillance_ode

Simulation of a compartmental infectious disease transmission model illustrating the impact of ID surveillance
simulate_sir_ode

Basic SIR model
simulate_sirdemographic_ode

Basic SIR model with births and deaths
simulate_reproductivenumber1_ode

Basic SIR model
run_model

A function that runs an app for specific settings and processes results for plot and text generation
simulate_reproductivenumber2_ode

Simulation of a compartmental infectious disease transmission model to study the reproductive number
simulate_directtransmission_ode

Simulation of a compartmental infectious disease transmission model illustrating different types of direct transmission
simulate_usanalysis_sir

Simulation to illustrate uncertainty and sensitivity analysis
simulate_sirdemographic_stochastic

Stochastic simulation of an SIR-type model with births and deaths
simulate_evolution_stochastic

Stochastic simulation of a compartmental SIR-type model with wild-type and mutant strains and treatment
simulate_modelexploration_sir

Simulation to illustrate parameter scan of the basic SIR model with births and deaths #'
simulate_maternalimmunity_ode

Simulation of a MSEIR model that represents a group of the population that is protected by disease through maternal antibodies
simulate_vectortransmission_ode

Vector transmission model