Reference

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