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DSAIRM (version 0.8.2)

Dynamical Systems Approach to Immune Response Modeling

Description

A collection of 'shiny' apps that allow for the simulation and exploration of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models. The development of this package was partially supported by NIH grant U19AI117891.

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Version

Install

install.packages('DSAIRM')

Monthly Downloads

295

Version

0.8.2

License

GPL-3

Issues

0

Pull Requests

0

Stars

34

Forks

15

Maintainer

Andreas Handel

Last Published

July 8th, 2019

Functions in DSAIRM (0.8.2)

simulate_modelvariants_ode

Simulation of a viral infection model with immune response The simulation illustrates different alternative models.
simulate_basicvirus_ode

Basic Virus model - ODE
simulate_usanalysis

Simulation to illustrate uncertainty and sensitivity analysis
simulate_basicbacteria_ode

Basic Bacteria model - ODE
simulate_virusandir_ode

Simulation of a viral infection model with an immune response
simulate_pkpdmodel_ode

PkPd Virus model
simulate_fit_confint

Fit a simple viral infection model and compute confidence intervals
simulate_fit_basicmodel

Fitting a simple viral infection models to influenza data
simulate_basicvirus_stochastic

Stochastic simulation of a compartmental acute virus infection model
simulate_drugresistance_stochastic

Stochastic simulation of a compartmental acute virus infection model with treatment and drug resistant strain
simulate_virusandtx_ode

Simulation of a basic viral infection model with drug treatment
simulate_modelexploration

Simulation to illustrate parameter scan of the basic bacteria model #'
simulate_fit_modelcomparison

Fitting 2 simple viral infection models to influenza data
generate_plotly

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

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

The main menu for the DSAIRM package
generate_shinyinput

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

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

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

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

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

DSAIRM: A package to learn about Dynamical Systems Approaches to Immune Response Modeling
simulate_basicbacteria_discrete

Basic Bacteria model - discrete