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DSAIRM (version 0.9.6)

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

270

Version

0.9.6

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/ahgroup/DSAIRM/

Homepage

https://ahgroup.github.io/DSAIRM/

Maintainer

Andreas Handel

Last Published

August 23rd, 2023

Functions in DSAIRM (0.9.6)

simulate_basicbacteria_ode

Basic Bacteria model - ODE

simulate_acutevirusir_ode

Acute Virus Infection and IR Model

simulate_modelvariants_ode

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

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_basicvirus_stochastic

Basic Virus Model

simulate_virusandtx_ode

Simulation of a basic viral infection model with drug treatment

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_extendedbacteria_ode

Extended Bacteria model - ODE

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

generate_modelsettings

A function to parse modelsettings for simulation runs

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

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

check_simresults

A function that checks if a call to simulation function worked

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_documentation

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

The main menu for the DSAIRM package

generate_plotly

A helper function that takes simulation results and produces plotly plots

simulate_basicvirus_fit

Fitting a simple viral infection models to influenza data

simulate_basicbacteria_modelexploration

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

simulate_basicvirus_modelexploration

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

Streptococcus pneumoniae infection data

simulate_bacteria_fit

Fitting a simple bacteria infection models to Streptococcus pneumoniae infection data

Influenza virus load data

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

simulate_basicbacteria_discrete

Basic Bacteria model - discrete