Learn R Programming

EpiModel (version 2.6.2)

Mathematical Modeling of Infectious Disease Dynamics

Description

Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, ).

Copy Link

Version

Install

install.packages('EpiModel')

Monthly Downloads

598

Version

2.6.2

License

GPL-3

Homepage

https://www.epimodel.org/

Maintainer

Samuel Jenness

Last Published

September 16th, 2026

Functions in EpiModel (2.6.2)

as.data.frame.dcm

Extract Model Data for Deterministic Compartmental Models

Update Either the "param" or "control" List

check_degdist_bal

Check Degree Distribution for Balance in Target Statistics

Create a TEA Variable for Infection Status for ndtv Animations

check_end_horizon_control

Check the format of the end.horizon control

dedup_cumulative_edgelist

Deduplicate a Cumulative Edgelist

Control Settings for Stochastic Network Models

create_scenario_list

Make a list of EpiModel scenarios from a data.frame of scenarios

create_dat_object

Create a Minimal netsim_dat Main List Object for a Network Model

Cross Checking of Inputs for Stochastic Individual Contact Models

Cross Checking of Inputs for Deterministic Compartmental Models

Control Settings for Stochastic Individual Contact Models

Control Settings for Deterministic Compartmental Models

Deterministic Compartmental Model Functions

departures.icm.bip

Departure: Bipartite icm Module

Plot Compartment Diagram for Epidemic Models

Delete Elements from Attribute List

Departures: netsim Module

copy_datattr_to_nwattr

Copy Vertex Attributes from the netsim_dat List to the Network Objects

Remove Edges That Include Specified Vertices

delete_vertices

Fast Version of network::delete.vertices for Edgelist-formatted Network

copy_nwattr_to_datattr

Copy Vertex Attributes From Network to netsim_dat List

Depart Nodes from the netsim_dat Object

generate_random_params

Generate Values for Random Parameters

ggplot2 Geom for Quantile Bands

Returns an adjacency list from an edge list

RColorBrewer Color Ramp for EpiModel Plots

Deterministic Compartmental Models

Cross Checking of Inputs for Stochastic Network Models

check_attr_lengths

Check that All Attributes in the Main netsim_dat Object are of Equal Length

Function to run the user-provided epi trackers

dissolution_coefs

Dissolution Coefficients for Stochastic Network Models

get_attr_history

Extract the Attributes History from Network Simulations

get_cumulative_edgelist

Get a Cumulative Edgelist From a Specified Network

Departure: icm Module

departures.2g.net

Departures: netsim Module

get_cumulative_edgelists_df

Get the Cumulative Edgelists of a Model

edgelist_censor

Table of Edge Censoring

edges_correct_eligible

Nodes Eligible to Form Ties for the Edges Correction

Adjustment for the Edges Coefficient with Changing Network Size

Get Arguments from EpiModel Parameterization Functions

Format One Parameter for Printing with the print.param.xxx Functions

discord_edgelist

Discordant Edgelist

get_connected_nodes

Returns all the node connected directly or indirectly to a set of nodes

get_cumulative_degree

Return the Cumulative Degree of a Set of Index Nodes

get_vertex_attribute

Get Vertex Attribute on Network Object

get_edgelists_df

Get the Edgelist(s) from the Specified Network(s)

Get an Edgelist From the Specified Network

Primary Infection Module for icm

Stochastic Individual Contact Models

get_degree_dist

Extract Degree Distributions from Network Diagnostics

get_formula_term_attr

Output ERGM Formula Attributes into a Character Vector

infection.2g.net

Primary Infection Module for netsim

get_discordant_edgelist

Get Discordant Edgelist Based on Specified Status Variable

Proportional Table of Vertex Attributes

Extract Network Objects from Network Simulations

get_network_attributes

Get Network Attributes from a Network Object

get_current_timestep

Return the Current Timestep

Get Individual Degree from Network or Edgelist

Extract the Parameter Set from Network Simulations

Extract Network Statistics from netsim or netdx Object

Return the Historical Contacts (Partners) of a Set of Index Nodes

Get the List of Modules

init_status.icm

Disease Status Initialization Module for icm

Extract Network Simulations

Modules for Stochastic Individual Contact Models

get_subnet_adj_list

Return an adjacency list of subnets

Primary Infection Module for netsim

init_status.net

Disease Status Initialization Module for netsim

Extract Transmissions Matrix from Network Epidemic Model

infection.icm.bip

Primary Infection Module for icm

Initial Conditions for Stochastic Network Models

Initialization: icm Module

Network Data and Stats Initialization

Write Out Test Progress to Console

make_stats_table

Create a Summary Table of Simulation Statistics

make_module_list

Populate the Module List After the Initialization Module is run

Initialization: netsim Module

get_network_term_attr

Output Network Attributes into a Character Vector

make_restart_point

Make a Lightweight Restart Point From a netsim Object with tergmLite

network_initialize

Initialize Network Object

netsim_cond_msg

Message to Find in Which Module a condition Occurred

increment_timestep

Increment the Current Timestep

Merge Data across Stochastic Individual Contact Model Simulations

Merge Model Simulations across netsim Objects

Extract Network Model Parameters

Group Numbers for Two-Group Network

Dynamic Network Updates

Initial Conditions for Deterministic Compartmental Models

Initial Conditions for Stochastic Individual Contact Models

is_active_unique_ids

Are These Nodes Active (Unique IDs)

Functions to Access and Edit the Main netsim_dat Object in Network Models

Plot Data from a Deterministic Compartmental Epidemic Model

netsim_error_logger

Handle the Logging of Traceback and Dumping of Frames on Error

Dynamic Network Model Estimation

Dynamic Network Model Diagnostics

Grow a Vector to a Given Size, Padding it With Empty Elements

Create a Value Sampler for Random Parameters

param.net_to_table

Coerce a list of parameters to a long.param.df

is_active_posit_ids

Are These Nodes Active (Positional IDs)

plot.epi.data.frame

Plot Epidemic Model Results From a Netsim Data.Frame

overwrite_attrs

Helper to use a data.frame to initialize some attributes

Add New Epidemiology Variables

Modules for Stochastic Network Models

Specify Controls by Network

Epidemic Parameters for Stochastic Network Models

Stochastic Network Models

param.net_from_table

Parameters List for Stochastic Network Models from a Formatted Data Frame

Epidemic Parameters for Deterministic Compartmental Models

Get Epidemic Output from icm Model

Epidemic Parameters for Stochastic Individual Contact Models

Print Method for ICM Objects

Utility Function for Printing netdx Object

Print Method for DCM Objects

Get Epidemic Output from netsim Model

Plot transmat Infection Tree in Three Styles

recovery.2g.net

Recovery: netsim Module

Recovery: icm Module

Plot Data from a Stochastic Network Epidemic Model

Recovery: netsim Module

recovery.icm.bip

Recovery: icm Module

reachable-nodes

Get the Forward or Backward Reachable Nodes for a Set of Nodes

Save Transmission Matrix

set_vertex_attribute

Set Vertex Attribute on Network Object

process_out.net

Save a List of netsim Data to Output List Format

Plot Dynamic Network Model Diagnostics

record_raw_object

Record an Arbitrary Object During a Simulation

record_attr_history

Record Attribute History

Remove a Set of Modules From the Module List

Plot Data from a Stochastic Individual Contact Epidemic Model

Resimulate Dynamic Network at Time 2+

Summary Model Statistics

Extract Summary Statistics of Networks Used in netsim

prevalence.icm.bip

Get Epidemic Output from icm Model

Save dcm Data to Output List Format

Stable Sampling Function

Save icm Data to Output List Format

tedgelist_cumulative_degree

Cumulative Degree of Each Node in a Timed Edgelist

Summary Model Statistics

update_dissolution

Adjust Dissolution Component of Network Model Fit

update_cumulative_edgelist

Update a Cumulative Edgelist of the Specified Network

Test the Model Output from a Stochastic Individual Contact Model

Set the List of Modules

tedgelist_to_toggles

Convert Timed Edgelist to Matrix of Toggles

unique_id-tools

Convert Unique Identifiers to/from Positional Identifiers

Truncate Simulation Time Series

Function to Reduce the Size of a netest Object

Set Network State During netsim Simulation

Initialize Networks Used in netsim

trigger_end_horizon

Function to Trigger the End Horizon

Simulate a Network for a Specified Number of Time Steps

Progress Print Module for Deterministic Compartmental Models

Progress Print Module for Stochastic Network Models

Print Method for Network Model Simulations

print_nwstats_table

Print Helper For Network Stats Tables

Progress Print Module for Stochastic Individual Contact Models

Summary Model Statistics

set_current_timestep

Set the Current Timestep

Apply a scenario object to a param.net object

update_unique_ids

Create the Unique Identifiers for New Nodes

Save netsim Data to Output List Format

Summary for Network Model Fit

Update Model Parameters for Stochastic Network Models

tedgelist_momentary_degree

Momentary Degree Distribution of a Timed Edgelist

Test the Model Output from a Network Model

Update List x Using the Elements of List new.x.

toggles_to_diss_stats

Convert Matrix of Toggles to Dissolution and Duration Statistics

Arrivals: netsim Module

InitErgmTerm.fuzzynodematch

Definition for fuzzynodematch ERGM Term

Fast Version of network::add.vertices for Edgelist-formatted Network

InitErgmTerm.absdiffby

Definition for absdiffby ERGM Term

InitErgmTerm.absdiffnodemix

Definition for absdiffnodemix ERGM Term

Apportion Using the Largest Remainder Method

as.phylo.transmat

Convert transmat Infection Tree into a phylo Object

as_tibble_edgelist

Convert an Edgelist into a Tibble

as.epi.data.frame

Validate and Convert to epi.data.frame

as.network.transmat

Convert transmat Infection Tree into a network Object

Arrive New Nodes to the netsim_dat Object

as_cumulative_edgelist

Convert an Object to a Cumulative Edgelist

arrivals.icm.bip

Arrivals: Bipartite icm Module

Arrivals: icm Module

EpiModel-package

Mathematical Modeling of Infectious Disease Dynamics

as.data.frame.icm

Extract Model Data for Stochastic Models

as.data.frame.netdx

Extract Timed Edgelists for netdx Objects

auto_update_attr

Update Vertex Attributes for Incoming Vertices

arrivals.2g.net

Arrivals: netsim Module