# Dynamical Systems Approach to Immune Response Modeling

## Documentation for package ‘DSAIRM’ version 0.8.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

DSAIRM-package | DSAIRM: A package to learn about Dynamical Systems Approaches to Immune Response Modeling
DSAIRM | DSAIRM: A package to learn about Dynamical Systems Approaches to Immune Response Modeling
dsairmmenu | The main menu for the DSAIRM package
generate_documentation | A helper function for the UI part of the Shiny apps
generate_fctcall | A helper function that produces a call to a simulator function 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 shiny UI elements
generate_text | A helper function that takes result from the simulators and produces text output
run_model | A function that runs an app for specific settings and processes results for plot and text generation
simulate_basicbacteria_discrete | Basic Bacteria model - discrete
simulate_basicbacteria_ode | Basic Bacteria model - ODE
simulate_basicvirus_ode | Basic Virus model - ODE
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_fit_basicmodel | Fitting a simple viral infection models to influenza data
simulate_fit_confint | Fit a simple viral infection model and compute confidence intervals
simulate_fit_modelcomparison | Fitting 2 simple viral infection models to influenza data
simulate_modelexploration | Simulation to illustrate parameter scan of the basic bacteria model #'
simulate_modelvariants_ode | Simulation of a viral infection model with immune response The simulation illustrates different alternative models.
simulate_pkpdmodel_ode | PkPd Virus model
simulate_usanalysis | Simulation to illustrate uncertainty and sensitivity analysis
simulate_virusandir_ode | Simulation of a viral infection model with an immune response
simulate_virusandtx_ode | Simulation of a basic viral infection model with drug treatment