Reference

All functions

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