Mathematical Modeling of Infectious Disease Dynamics
Extract Network Statistics from netsim or netdx Object
Get Vertex Attribute on Network Object
Definition for absdiffby ERGM Term
Definition for absdiffnodemix ERGM Term
Utility Function for Printing netdx Object
Save a List of netsim Data to Output List Format
Get the Forward or Backward Reachable Nodes for a Set of Nodes
Save dcm Data to Output List Format
Save icm Data to Output List Format
Save netsim Data to Output List Format
Set the Current Timestep
Set the List of Modules
Set Network State During netsim Simulation
Save Transmission Matrix
Set Vertex Attribute on Network Object
Initialize Networks Used in netsim
Simulate a Network for a Specified Number of Time Steps
Stable Sampling Function
Extract Summary Statistics of Networks Used in netsim
Summary Model Statistics
Summary Model Statistics
Summary for Network Model Fit
Convert Unique Identifiers to/from Positional Identifiers
Update a Cumulative Edgelist of the Specified Network
Adjust Dissolution Component of Network Model Fit
Update List x Using the Elements of List new.x.
Update Model Parameters for Stochastic Network Models
Create the Unique Identifiers for New Nodes
Apply a scenario object to a param.net object
Progress Print Module for Deterministic Compartmental Models
Progress Print Module for Stochastic Individual Contact Models
Progress Print Module for Stochastic Network Models
Extract Model Data for Deterministic Compartmental Models
RColorBrewer Color Ramp for EpiModel Plots
Check that All Attributes in the Main netsim_dat Object are of Equal...
Cross Checking of Inputs for Stochastic Network Models
Discordant Edgelist
Dissolution Coefficients for Stochastic Network Models
Get the Cumulative Edgelists of a Model
Return the Current Timestep
Epidemic Parameters for Stochastic Individual Contact Models
Parameters List for Stochastic Network Models from a Formatted Data Fr...
Coerce a list of parameters to a long.param.df
Epidemic Parameters for Stochastic Network Models
Plot Data from a Deterministic Compartmental Epidemic Model
Plot Epidemic Model Results From a Netsim Data.Frame
Plot Data from a Stochastic Individual Contact Epidemic Model
Plot Dynamic Network Model Diagnostics
Plot Data from a Stochastic Network Epidemic Model
Plot transmat Infection Tree in Three Styles
Get Epidemic Output from icm Model
Extract Network Model Parameters
Departures: netsim Module
Disease Status Initialization Module for icm
Grow a Vector to a Given Size, Padding it With Empty Elements
Get Epidemic Output from icm Model
Fast Version of network::add.vertices for Edgelist-formatted Network
Apportion Using the Largest Remainder Method
Arrivals: netsim Module
Arrivals: Bipartite icm Module
Arrivals: icm Module
Arrivals: netsim Module
Arrive New Nodes to the netsim_dat Object
Convert an object to a cumulative_edgelist
Convert an Edgelist into a Tibble
Cross Checking of Inputs for Stochastic Individual Contact Models
Extract Model Data for Stochastic Models
Extract Timed Edgelists for netdx Objects
Validate and Convert to epi.data.frame
Convert transmat Infection Tree into a network Object
Convert transmat Infection Tree into a phylo Object
Update Vertex Attributes for Incoming Vertices
Departures: netsim Module
Check Degree Distribution for Balance in Target Statistics
Check the format of the end.horizon control
Create a TEA Variable for Infection Status for ndtv Animations
Update Either the "param" or "control" List
Plot Compartment Diagram for Epidemic Models
Control Settings for Deterministic Compartmental Models
Departure: Bipartite icm Module
Control Settings for Stochastic Individual Contact Models
Control Settings for Stochastic Network Models
Copy Vertex Attributes from the netsim_dat List to the Network Objec...
Copy Vertex Attributes From Network to netsim_dat List
Create a Minimal netsim_dat Main List Object for a Network Model
Make a list of EpiModel scenarios from a data.frame of scenarios
Cross Checking of Inputs for Deterministic Compartmental Models
Departure: icm Module
Deterministic Compartmental Model Functions
Deterministic Compartmental Models
Deduplicate a cumulative edgelist by combining overlapping edges
Delete Elements from Attribute List
Remove Edges That Include Specified Vertices
Fast Version of network::delete.vertices for Edgelist-formatted Networ...
Depart Nodes from the netsim_dat Object
Table of Edge Censoring
Adjustment for the Edges Coefficient with Changing Network Size
Function to run the user-provided epi trackers
Mathematical Modeling of Infectious Disease Dynamics
EpiModel Web
Format One Parameter for Printing with the print.param.xxxFunctions
Return the Cumulative Degree of a Set of Index Nodes
Generate Values for Random Parameters
ggplot2 Geom for Quantile Bands
Returns an adjacency list from an edge list
Get Arguments from EpiModel Parameterization Functions
Extract the Attributes History from Network Simulations
Proportional Table of Vertex Attributes
Returns all the node connected directly or indirectly to a set of node...
Get a Cumulative Edgelist From a Specified Network
Get Individual Degree from Network or Edgelist
Get Discordant Edgelist Based on Specified Status Variable
Get an Edgelist From the Specified Network
Get the Edgelist(s) from the Specified Network(s)
Output ERGM Formula Attributes into a Character Vector
Get the List of Modules
Get Network Attributes from a Network Object
Output Network Attributes into a Character Vector
Extract Network Objects from Network Simulations
Extract the Parameter Set from Network Simulations
Return the Historical Contacts (Partners) of a Set of Index Nodes
Extract Network Simulations
Return an adjacency list of subnets
Extract Transmissions Matrix from Network Epidemic Model
Stochastic Individual Contact Models
Group Numbers for Two-Group Network
Increment the Current Timestep
Primary Infection Module for netsim
Primary Infection Module for icm
Primary Infection Module for icm
Primary Infection Module for netsim
Network Data and Stats Initialization
Disease Status Initialization Module for netsim
Initial Conditions for Deterministic Compartmental Models
Initial Conditions for Stochastic Individual Contact Models
Initial Conditions for Stochastic Network Models
Get Epidemic Output from netsim Model
Definition for fuzzynodematch ERGM Term
Initialization: icm Module
Initialization: netsim Module
Are These Nodes Active (Positional IDs)
Are These Nodes Active (Unique IDs)
Populate the Module List After the Initialization Module is run
Create a Summary Table of Simulation Statistics
Write Out Test Progress to Console
Print Helper For Network Stats Tables
Merge Data across Stochastic Individual Contact Model Simulations
Merge Model Simulations across netsim Objects
Modules for Stochastic Individual Contact Models
Modules for Stochastic Network Models
Specify Controls by Network
Create a Value Sampler for Random Parameters
Add New Epidemiology Variables
Functions to Access and Edit the Main netsim_dat Object in Network Mod...
Dynamic Network Model Diagnostics
Dynamic Network Model Estimation
Message to Find in Which Module a condition Occurred
Handle the Logging of Traceback and Dumping of Frames on Error
Stochastic Network Models
Initialize Network Object
Dynamic Network Updates
Helper to use a data.frame to initialize some attributes
Epidemic Parameters for Deterministic Compartmental Models
Record Attribute History
Record an Arbitrary Object During a Simulation
Recovery: netsim Module
Recovery: icm Module
Recovery: icm Module
Recovery: netsim Module
Remove a Set of Modules From the Module List
Resimulate Dynamic Network at Time 2+
Summary Model Statistics
Convert Timed Edgelist to Matrix of Toggles
Test the Model Output from a Stochastic Individual Contact Model
Test the Model Output from a Network Model
Convert Matrix of Toggles to Dissolution and Duration Statistics
Function to Trigger the End Horizon
Function to Reduce the Size of a netest Object
Truncate Simulation Time Series
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, <doi:10.18637/jss.v084.i08>).
Useful links