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DSAIDE (version 0.8.3)

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

Description

Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios. The purpose of the package is to help individuals learn about infectious disease epidemiology (ecology/evolution) 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

0.8.3

License

GPL-3

Issues

0

Pull Requests

0

Stars

26

Forks

18

Maintainer

Andreas Handel

Last Published

January 9th, 2020

Functions in DSAIDE (0.8.3)

simulate_idcontrol_ode

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

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

Fitting a simple SIR type model to norovirus outbreak data
simulate_usanalysis_sir

Simulation to illustrate uncertainty and sensitivity analysis
simulate_fit_flu

Fitting a SIR-type model to flu data
simulate_sirdemographic_stochastic

Stochastic simulation of an SIR-type model with births and deaths
simulate_reproductivenumber2_ode

Simulation of a compartmental infectious disease transmission model to study the reproductive number
simulate_reproductivenumber1_ode

Basic SIR model
simulate_maternalimmunity_ode

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

Cases of norovirus during an outbreak
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_evolution_stochastic

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

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

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

Environmental Transmission model
simulate_sirdemographic_ode

Basic SIR model with births and deaths
simulate_idsurveillance_ode

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

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

Basic SIR model
simulate_idcharacteristics_ode

Simulation of an infectious disease transmission model with multiple compartments
simulate_seir_stochastic

Stochastic simulation of an SEIR-type model
simulate_sir_discrete

Basic discrete time SIR model
simulate_vectortransmission_ode

Vector transmission model
generate_ggplot

A helper function that takes simulation results and produces ggplot plots
dsaidemenu

The main menu for the DSAIDE package
generate_text

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

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

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

A helper function that takes simulation results and produces plotly plots
flu1918data

1918 Influenza mortality data
generate_shinyinput

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

A helper function which processes and displays the documentation part for each app