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DSAIDE (version 0.9.6)

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

0.9.6

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/ahgroup/DSAIDE/

Homepage

https://ahgroup.github.io/DSAIDE/

Maintainer

Andreas Handel

Last Published

August 23rd, 2023

Functions in DSAIDE (0.9.6)

The main menu for the DSAIDE package

simulate_idcontrolmultigroup_ode

Simulation of a compartmental infectious disease transmission model with 3 types of hosts and intervention

simulate_Drug_Resistance_Evolution_stochastic

Drug Resistance Evolution

simulate_idpatterns_ode

Simulation of a compartmental infectious disease transmission model including seasonality

simulate_noro_fit

Fitting a simple SIR type model to norovirus outbreak data

simulate_idsurveillance_ode

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

simulate_Complex_ID_Control_ode

Complex ID Control

simulate_Environmental_Transmission_model_ode

Environmental Transmission model

simulate_Host_Heterogeneity_Model_ode

Host Heterogeneity Model

generate_ggplot

A helper function that takes simulation results and produces ggplot plots

generate_fctcall

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

simulate_directtransmission_ode

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

simulate_SIRSd_model_ode

simulate_idcontrolmultioutbreak_ode

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

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

simulate_flu_fit

Fitting a SIR-type model to flu data

simulate_Vector_transmission_model_ode

Vector transmission model

simulate_SIR_usanalysis

Simulation to illustrate uncertainty and sensitivity analysis

simulate_idvaccine_ode

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

simulate_Characteristics_of_ID_ode

Characteristics of ID

simulate_SIR_modelexploration

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_SIR_model_ode

Cases of norovirus during an outbreak

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

generate_plotly

A helper function that takes simulation results and produces plotly plots

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

simulate_SIR_model_discrete

simulate_SEIRSd_model_stochastic

simulate_SIRSd_model_stochastic

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