Dynamical Systems Approach to Immune Response Modeling

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Documentation for package ‘DSAIRM’ version 0.9.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

check_simresults	A function that checks if a call to simulation function worked
dsairmmenu	The main menu for the DSAIRM package
generate_documentation	A helper function which processes and displays the documentation part for each app
generate_fctcall	A helper function that produces a call to a simulator function for specific settings
generate_ggplot	A helper function that takes simulation results and produces ggplot plots
generate_modelsettings	A function to parse modelsettings for simulation runs
generate_plotly	A helper function that takes simulation results and produces plotly 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
hayden96flu	Influenza virus load data
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_acutevirusir_ode	Acute Virus Infection and IR Model
simulate_bacteria_fit	Fitting a simple bacteria infection models to Streptococcus pneumoniae infection data
simulate_basicbacteria_discrete	Basic Bacteria model - discrete
simulate_basicbacteria_modelexploration	Simulation to illustrate parameter scan of the basic bacteria model #'
simulate_basicbacteria_ode	Basic Bacteria model - ODE
simulate_basicvirus_fit	Fitting a simple viral infection models to influenza data
simulate_basicvirus_modelexploration	Simulation to illustrate parameter scan of the basic virus model #'
simulate_basicvirus_ode	Basic Virus Model
simulate_basicvirus_stochastic	Basic Virus Model
simulate_chronicvirusir_ode	Chronic Virus Infection and IR Model
simulate_confint_fit	Fit a simple viral infection model and compute confidence intervals
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_fludrug_fit	Fitting a simple viral infection model with 2 types of drug mechanisms to influenza data
simulate_modelcomparison_fit	Fitting 2 simple viral infection models to influenza data
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