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EpiModel (version 2.4.0)

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, ).

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Version

Install

install.packages('EpiModel')

Monthly Downloads

933

Version

2.4.0

License

GPL-3

Maintainer

Samuel Jenness

Last Published

June 20th, 2023

Functions in EpiModel (2.4.0)

auto_update_attr

Update Vertex Attributes for Incoming Vertices

as.network.transmat

Convert transmat Infection Tree into a network Object

as.phylo.transmat

Convert transmat Infection Tree into a phylo Object

as.data.frame.netdx

Extract Timed Edgelists for netdx Objects

as.data.frame.icm

Extract Model Data for Stochastic Models

Arrive New Nodes to the netsim_dat Object

RColorBrewer Color Ramp for EpiModel Plots

as.data.frame.dcm

Extract Model Data for Deterministic Compartmental Models

Control Settings for Stochastic Network Models

Control Settings for Stochastic Individual Contact Models

check_degdist_bal

Check Degree Distribution for Balance in Target Statistics

create_dat_object

Create a Minimal netsim_dat Main List Object for a Network Model

copy_nwattr_to_datattr

Copy Vertex Attributes From Network to netsim_dat List

Create a TEA Variable for Infection Status for ndtv Animations

Update Either the "param" or "control" List

Control Settings for Deterministic Compartmental Models

check_end_horizon_control

Check the format of the end.horizon control

Plot Compartment Diagram for Epidemic Models

copy_datattr_to_nwattr

Copy Vertex Attributes from the netsim_dat List to the Network Objects

create_scenario_list

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

check_attr_lengths

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

Cross Checking of Inputs for Deterministic Compartmental Models

Cross Checking of Inputs for Stochastic Individual Contact Models

Cross Checking of Inputs for Stochastic Network Models

discord_edgelist

Discordant Edgelist

Depart Nodes from the netsim_dat Object

Departures: netsim Module

Delete Elements from Attribute List

Departure: icm Module

Delete Elements from Attribute List

Adjustment for the Edges Coefficient with Changing Network Size

Function to run the user-provided epi trackers

Remove Edges That Include Specified Vertices

departures.2g.net

Departures: netsim Module

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

Get the List of Modules

departures.icm.bip

Departure: Bipartite icm Module

Extract Network Objects from Network Simulations

generate_random_params

Generate Values for Random Parameters

Deterministic Compartmental Model Functions

get_network_attributes

Get Network Attributes from a Network Object

get_cumulative_edgelist

Get a Cumulative Edgelist From a Specified Network

Deterministic Compartmental Models

get_cumulative_edgelists_df

Get the Cumulative Edgelists of a Model

dissolution_coefs

Dissolution Coefficients for Stochastic Network Models

Proportional Table of Vertex Attributes

init_status.icm

Disease Status Initialization Module for icm

edgelist_censor

Table of Edge Censoring

increment_timestep

Increment the Current Timestep

get_cumulative_degree

Return the Cumulative Degree of a Set of Index Nodes

get_formula_term_attr

Output ERGM Formula Attributes into a Character Vector

Get an Edgelist From the Specified Network

init_status.net

Disease Status Initialization Module for netsim

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

Extract the Parameter Set from Network Simulations

Extract Network Statistics from netsim or netdx Object

Group Numbers for Two-Group Network

ggplot2 Geom for Quantile Bands

Extract Network Model Parameters

delete_vertices

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

Extract Network Simulations

Get Arguments from EpiModel Parameterization Functions

get_vertex_attribute

Get Vertex Attribute on Network Object

get_network_term_attr

Output Network Attributes into a Character Vector

Initial Conditions for Deterministic Compartmental Models

Initial Conditions for Stochastic Individual Contact Models

Stochastic Individual Contact Models

Specify Controls by Network

Modules for Stochastic Network Models

Merge Model Simulations across netsim Objects

Dynamic Network Updates

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

Primary Infection Module for netsim

infection.icm.bip

Primary Infection Module for icm

Add New Epidemiology Variables

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

Get Individual Degree from Network or Edgelist

get_attr_history

Extract the Attributes History from Network Simulations

get_current_timestep

Return the Current Timestep

Modules for Stochastic Individual Contact Models

make_stats_table

Create a Summary Table of Simulation Statistics

make_module_list

Populate the Module List After the Initialization Module is run

Extract Transmissions Matrix from Network Epidemic Model

Initial Conditions for Stochastic Network Models

Dynamic Network Model Diagnostics

Create a Value Sampler for Random Parameters

param.net_from_table

Parameters List for Stochastic Network Models from a Formatted Data Frame

infection.2g.net

Primary Infection Module for netsim

Plot transmat Infection Tree in Three Styles

record_attr_history

Record Attribute History

record_raw_object

Record an Arbitrary Object During a Simulation

Plot Dynamic Network Model Diagnostics

Plot Data from a Stochastic Network Epidemic Model

Save dcm Data to Output List Format

Plot Data from a Stochastic Individual Contact Epidemic Model

Dynamic Network Model Estimation

Epidemic Parameters for Stochastic Network Models

Resimulate Dynamic Network at Time 2+

set_current_timestep

Set the Current Timestep

Primary Infection Module for icm

print_nwstats_table

Print Helper For Network Stats Tables

Set the List of Modules

process_out.net

Save a List of netsim Data to Output List Format

Stable Sampling Function

Simulate a Network for a Specified Number of Time Steps

netsim_error_logger

Handle the Logging of Traceback and Dumping of Frames on Error

Network Data and Stats Initialization

Initialization: icm Module

Initialization: netsim Module

Merge Data across Stochastic Individual Contact Model Simulations

Progress Print Module for Stochastic Individual Contact Models

recovery.icm.bip

Recovery: icm Module

Write Out Test Progress to Console

set_vertex_attribute

Set Vertex Attribute on Network Object

Recovery: netsim Module

unique_id-tools

Convert Unique Identifiers to/from Positional Identifiers

update_cumulative_edgelist

Update a Cumulative Edgelist of the Specified Network

is_active_posit_ids

Are These Nodes Active (Positional IDs)

Update Model Parameters for Stochastic Network Models

Stochastic Network Models

netsim_cond_msg

Message to Find in Which Module a condition Occurred

network_initialize

Initialize Network Object

is_active_unique_ids

Are These Nodes Active (Unique IDs)

Initialize Networks Used in netsim

Plot Data from a Deterministic Compartmental Epidemic Model

Get Epidemic Output from icm Model

prevalence.icm.bip

Get Epidemic Output from icm Model

Get Epidemic Output from netsim Model

update_unique_ids

Create the Unique Identifiers for New Nodes

Save icm Data to Output List Format

Epidemic Parameters for Deterministic Compartmental Models

Summary Model Statistics

Summary Model Statistics

Test the Model Output from a Stochastic Individual Contact Model

Progress Print Module for Stochastic Network Models

Recovery: icm Module

recovery.2g.net

Recovery: netsim Module

Save netsim Data to Output List Format

Remove a Set of Modules From the Module List

Objects exported from other packages

Epidemic Parameters for Stochastic Individual Contact Models

Apply a scenario object to a param.net object

Progress Print Module for Deterministic Compartmental Models

Test the Model Output from a Network Model

Summary for Network Model Fit

Utility Function for Printing netdx Object

toggles_to_diss_stats

Convert Matrix of Toggles to Dissolution and Duration Statistics

Save Transmission Matrix

Function to Reduce the Size of a netest Object

Set Network State During netsim Simulation

trigger_end_horizon

Function to Trigger the End Horizon

Truncate Simulation Time Series

Summary Model Statistics

update_dissolution

Adjust Dissolution Component of Network Model Fit

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

tedgelist_to_toggles

Convert Timed Edgelist to Matrix of Toggles

Extract Summary Statistics of Networks Used in netsim

InitErgmTerm.absdiffby

Definition for absdiffby ERGM Term

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

InitErgmTerm.absdiffnodemix

Definition for absdiffnodemix ERGM Term

EpiModel-package

Mathematical Modeling of Infectious Disease Dynamics

InitErgmTerm.fuzzynodematch

Definition for fuzzynodematch ERGM Term

Apportion Using the Largest Remainder Method

Arrivals: icm Module

arrivals.icm.bip

Arrivals: Bipartite icm Module

Arrivals: netsim Module

arrivals.2g.net

Arrivals: netsim Module