Function reference • idmodelr

Datasets Datasets built into the package. These include details of implemented models and common parameters.
`model_details`	Model Details
`parameter_details`	Parameter Details
Deterministic Compartmental Models Deterministic compartmental ODE models potentially including demographic processes, vaccination, and/or risk stratification etc. See documentation and `model_details` for information.
`SEI_ode()`	Susceptible-Exposed-Infected Model
`SI_ode()`	Susceptible-Infected Model
`SEIRS_ode()`	Susceptible-Exposed-Infected-Recovered-Susceptible Model
`SEIS_ode()`	Susceptible-Exposed-Infected-Susceptible Model
`SIRS_ode()`	Susceptible-Infected-Recovered-Susceptible Model
`SIS_ode()`	Susceptible-Infected-Susceptible Model
`SEIR_ode()`	Susceptible-Exposed-Infected-Recovered Model
`SHLIR_ode()`	Susceptible-High-risk-latent-Low-risk-latent-Infected-Recovered Model
`SHLITR_ode()`	Susceptible-High-risk-latent-Low-risk-latent-Infected-Treated-Recovered Model
`SIR_ode()`	Susceptible-Infected-Recovered Model
`SIRS_vaccination_ode()`	Susceptible-Infected-Recovered-Susceptible Model with Vaccination
`SIR_vaccination_ode()`	Susceptible-Infected-Recovered Model with Vaccination
`SHLITR_risk_ode()`	Susceptible-High-risk-latent-Low-risk-latent-Infected-Treated-Recovered Model, Stratified by Risk
`SEIRS_demographics_ode()`	Susceptible-Exposed-Infected-Recovered-Susceptible Model with Simple Demographics
`SEIR_demographics_ode()`	Susceptible-Exposed-Infected-Recovered Model with Simple Demographics
`SEIS_demographics_ode()`	Susceptible-Exposed-Infected-Susceptible Model with Simple Demographics
`SEI_demographics_ode()`	Susceptible-Exposed-Infected Model with Simple Demographics
`SHLIR_demographics_ode()`	Susceptible-High-risk-latent-Low-risk-latent-Infected-Recovered Model with Simple Demographics
`SHLITR_demographics_ode()`	Susceptible-High-risk-latent-Low-risk-latent-Infected-Treated-Recovered Model with Simple Demographics
`SHLITR_risk_demographics_ode()`	Susceptible-High-risk-latent-Low-risk-latent-Infected-Treated-Recovered Model with Demographics, Stratified by Risk
`SIRS_demographics_ode()`	Susceptible-Infected-Recovered-Susceptible Model with Simple Demographics
`SIRS_vaccination_demographics_ode()`	Susceptible-Infected-Recovered-Susceptible Model with Simple Demographics and Vaccination
`SIR_demographics_ode()`	Susceptible-Infected-Recovered Model with Simple Demographics
`SIR_vaccination_demographics_ode()`	Susceptible-Infected-Recovered Model with Simple Demographics and Vaccination
`SIS_demographics_ode()`	Susceptible-Infected-Susceptible Model with Simple Demographics
`SI_demographics_ode()`	Susceptible-Infected Model with Simple Demographics
Simulation Utilities Functions for solving, simulating, and summarising ID models.
`solve_ode()`	A Simple Wrapper for lsoda
`simulate_model()`	A Function to Simulate a Model from a Generic Simulation Function, with Pre and Post Processing
`summarise_model()`	Summarise a Model Simulation
Plotting Utilities Functions for plotting ID models
`plot_model()`	Plot Compartment Populations over Time for a Model Simulation
Workflow Utilities Functions to streamline the workflow of using ID models. These include random parameter set generation, scenario analysis and estimation of normal distrubutions based on published information.
`required_parameters()`	Lookup the Details of Parameters Required by a Model
`generate_parameter_permutations()`	A Function to Generate Parameter Permutations
`scenario_analysis()`	A Function to Perform Scenario Analysis for a Generic Model Object.
`estimate_norm_dist_from_ci()`	A Function to Estimate a Normal Distribution from Credible or Confidence Intervals
Munging Utilities Functions to facilitate munging (i.e manipulation) of ID model simulations
`gather_strat_multi_variable()`	A Function to Gather Multiple Stratified Variables into a Tidy Format
`gather_strat_variable()`	A Function to Gather a Stratified Variable into a Tidy Format
`aggregate_model()`	A Function to Apply Multiple Aggregations to Model Output
`aggregate_model_internal()`	An Internal Function to Aggregate Model Output Using other Idmodelr functions.
`combine_strat_model_output()`	Reduces the Dimensionality of a Stratified Model
`combine_to_age_model()`	Combine an Infectious Disease Model To a Demographic Model
`model_df_to_vector()`	Extracts a Single Column, Summarises if from Simulation
`add_pointer_struct()`	Adds Pointer Structure to R objects
`summarise_strat_var()`	Sum a Stratified Variable
`summarise_var_by_strat()`	Sum a Stratified Variable by Stratification Level

Reference

Datasets

Deterministic Compartmental Models

Simulation Utilities

Plotting Utilities

Workflow Utilities

Munging Utilities