Dynamical Systems Approach to Infectious Disease Epidemiology


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Documentation for package ‘DSAIDE’ version 0.8.0

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DSAIDE-package DSAIDE: A package to learn about Dynamical Systems Approaches to Infectious Disease Epidemiology
DSAIDE DSAIDE: A package to learn about Dynamical Systems Approaches to Infectious Disease Epidemiology
dsaidemenu The main menu for the DSAIDE package
generate_documentation A helper function for the UI part of the Shiny apps
generate_fctcall A function that produces a call to a simulator functions for specific settings
generate_ggplot A helper function that takes result from the simulators and produces plots
generate_plotly A helper function that takes result from the simulators and produces plots
generate_shinyinput A helper function that takes a model and generates the shiny UI elements for the analyze tab
generate_text A helper function that takes result from the simulators and produces text output
run_model A function that runs a DSAIRM/DSAIDE app
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_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_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_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_reproductivenumber_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