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DSAIRM (version 1.0.0)

Dynamical Systems Approach to Immune Response Modeling

Description

Simulation models (apps) 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.

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Version

Install

install.packages('DSAIRM')

Monthly Downloads

391

Version

1.0.0

License

GPL-3

Issues

0

Pull Requests

0

Stars

34

Forks

14

Maintainer

Andreas Handel

Last Published

July 9th, 2026

Functions in DSAIRM (1.0.0)

simulate_modelvariants_ode

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

Fit a simple viral infection model and compute confidence intervals
simulate_chronicvirusir_ode

Chronic Virus Infection and IR Model
simulate_drugresistance_stochastic

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

Fitting 2 simple viral infection models to influenza data
simulate_fludrug_fit

Fitting a simple viral infection model with 2 types of drug mechanisms to influenza data
simulate_basicvirus_ode

Basic Virus Model
simulate_pkpdmodel_ode

PkPd Virus model
simulate_extendedbacteria_ode

Extended Bacteria model - ODE
simulate_basicvirus_stochastic

Basic Virus Model
simulate_virusandtx_ode

Simulation of a basic viral infection model with drug treatment
simulate_virusandir_ode

Simulation of a viral infection model with an immune response
simulate_usanalysis

Simulation to illustrate uncertainty and sensitivity analysis
generate_documentation

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

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

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

The main menu for the DSAIRM package
generate_text

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

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

A function to parse modelsettings for simulation runs
generate_fctcall

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

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

A function that checks if a call to simulation function worked
run_model

A function that runs an app for specific settings and processes results for plot and text generation
schirm20strep

Streptococcus pneumoniae infection data
simulate_basicvirus_fit

Fitting a simple viral infection models to influenza data
simulate_basicbacteria_discrete

Basic Bacteria model - discrete
simulate_bacteria_fit

Fitting a simple bacteria infection models to Streptococcus pneumoniae infection data
hayden96flu

Influenza virus load data
simulate_basicbacteria_ode

Basic Bacteria model - ODE
simulate_basicvirus_modelexploration

Simulation to illustrate parameter scan of the basic virus model #'
simulate_basicbacteria_modelexploration

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

Acute Virus Infection and IR Model