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EpiModel (version 2.3.1)

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

2.3.1

License

GPL-3

Maintainer

Samuel Jenness

Last Published

October 1st, 2022

Functions in EpiModel (2.3.1)

as.data.frame.dcm

Extract Model Data for Deterministic Compartmental Models
as.network.transmat

Convert transmat Infection Tree into a network Object
as.phylo.transmat

Convert transmat Infection Tree into a phylo Object
check_degdist_bal

Check Degree Distribution for Balance in Target Statistics
as.data.frame.icm

Extract Model Data for Stochastic Models
as.data.frame.netdx

Extract Timed Edgelists for netdx Objects
color_tea

Create a TEA Variable for Infection Status for ndtv Animations
auto_update_attr

Update Vertex Attributes for Incoming Vertices
create_dat_object

Create a Minimal Main List Object for a Network Model
control.icm

Control Settings for Stochastic Individual Contact Models
comp_plot

Plot Compartment Diagram for Epidemic Models
brewer_ramp

RColorBrewer Color Ramp for EpiModel Plots
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 Object are of Equal Length
crosscheck.dcm

Cross Checking of Inputs for Deterministic Compartmental Models
control.dcm

Control Settings for Deterministic Compartmental Models
common_updater

Update Either the "param" or "control" List
control.net

Control Settings for Stochastic Network Models
delete_vertices

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

Copy Vertex Attributes from the dat List to the Network Object
departures.icm

Departure: icm Module
delete_attr

Delete Elements from Attribute List
departures.2g.net

Departures: netsim Module
copy_nwattr_to_datattr

Copy Vertex Attributes From Network to dat List
generate_random_params

Generate Values for Random Parameters
dissolution_coefs

Dissolution Coefficients for Stochastic Network Models
crosscheck.icm

Cross Checking of Inputs for Stochastic Individual Contact Models
deleteAttr

Delete Elements from Attribute List
crosscheck.net

Cross Checking of Inputs for Stochastic Network Models
discord_edgelist

Discordant Edgelist
get_attr_history

Extract the Attributes History from Network Simulations
epiweb

EpiModel Web
edges_correct

Adjustment for the Edges Coefficient with Changing Network Size
departures.net

Departures: netsim Module
geom_bands

ggplot2 Geom for Quantile Bands
epi_trackers

Function to run the user-provided epi trackers
dcm.mods

Deterministic Compartmental Model Functions
get_args

Get Arguments from EpiModel Parameterization Functions
get_cumulative_edgelist

Get a Cumulative Edgelist From a Specified Network
dcm

Deterministic Compartmental Models
departures.icm.bip

Departure: Bipartite icm Module
get_partners

Return the Historical Partners (Contacts) of a Set of Index Patients
get_attr_prop

Proportional Table of Vertex Attributes
get_sims

Extract Network Simulations
get_param_set

Extract the Parameter Set from Network Simulations
get_formula_term_attr

Output ERGM Formula Attributes into a Character Vector
get_network

Extract networkDynamic and network Objects from Network Simulations
get_nwstats

Extract Network Statistics from netsim or netdx Object
format_param

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

Table of Edge Censoring
get_current_timestep

Return the Current Timestep
get_cumulative_edgelists_df

Get the Cumulative Edgelists of a Model
get_edgelist

Get an Edgelist From the Specified Network
get_degree

Get Individual Degree from Network or Edgelist
is.transmat

Extract Transmissions Matrix from Network Epidemic Model
get_network_term_attr

Output Network Attributes into a Character Vector
infection.icm

Primary Infection Module for icm
init_status.icm

Disease Status Initialization Module for icm
icm

Stochastic Individual Contact Models
infection.icm.bip

Primary Infection Module for icm
idgroup

Group Numbers for Two-Group Network
get_nwparam

Extract Network Model Parameters
get_vertex_attribute

Get Vertex Attribute on Network Object
increment_timestep

Increment the Current Timestep
merge.icm

Merge Data across Stochastic Individual Contact Model Simulations
mcat

Write Out Test Progress to Console
init.dcm

Initial Conditions for Deterministic Compartmental Models
infection.2g.net

Primary Infection Module for netsim
init_status.net

Disease Status Initialization Module for netsim
is_active_posit_ids

Are These Nodes Active (Positional IDs)
modules.icm

Modules for Stochastic Individual Contact Models
infection.net

Primary Infection Module for netsim
init_tergmLite

Initialize EpiModel netsim Object for tergmLite Simulation
is_active_unique_ids

Are These Nodes Active (Unique IDs)
make_stats_table

Create a Summary Table of Simulation Statistics
merge.netsim

Merge Model Simulations across netsim Objects
initialize.net

Initialization: netsim Module
initialize.icm

Initialization: icm Module
init.net

Initial Conditions for Stochastic Network Models
init.icm

Initial Conditions for Stochastic Individual Contact Models
networkLitemethods

networkLite Methods
network_initialize

Initialize Network Object
net-accessor

Functions to Access and Edit the Main List Object in Network Models
networkLite

networkLite Constructor Utilities
modules.net

Modules for Stochastic Network Models
netsim_cond_msg

Message to Find in Which Module a condition Occurred
netdx

Dynamic Network Model Diagnostics
mutate_epi

Add New Epidemiology Variables
netest

Dynamic Network Model Estimation
plot.dcm

Plot Data from a Deterministic Compartmental Epidemic Model
param.net_from_table

Parameters List for Stochastic Network Models from a Formatted Data Frame
plot.netsim

Plot Data from a Stochastic Network Epidemic Model
plot.netdx

Plot Dynamic Network Model Diagnostics
param.dcm

Epidemic Parameters for Deterministic Compartmental Models
nwupdate.net

Dynamic Network Updates
param.net

Epidemic Parameters for Stochastic Network Models
netsim

Stochastic Network Models
param.icm

Epidemic Parameters for Stochastic Individual Contact Models
param_random

Create a Value Sampler for Random Parameters
saveout.net

Save netsim Data to Output List Format
ssample

Stable Sampling Function
sim_nets_t1

Simulate Initial Network at Time 1 for Model Initialization
update_dissolution

Adjust Dissolution Component of Network Model Fit
summary.dcm

Summary Model Statistics
saveout.dcm

Save dcm Data to Output List Format
saveout.icm

Save icm Data to Output List Format
prevalence.icm.bip

Get Epidemic Output from icm Model
plot.icm

Plot Data from a Stochastic Individual Contact Epidemic Model
update_list

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

Update Model Parameters for Stochastic Network Models
record_attr_history

Record Attribute History
set_vertex_attribute

Set Vertex Attribute on Network Object
prevalence.net

Get Epidemic Output from netsim Model
record_raw_object

Record an Arbitrary Object During a Simulation
process_out.net

Save a List of netsim Data to Output List Format
plot.transmat

Plot transmat Infection Tree in Three Styles
recovery.2g.net

Recovery: netsim Module
recovery.net

Recovery: netsim Module
set_transmat

Save Transmission Matrix
test_net

Test the Model Output from a Network Model
use_scenario

Apply a scenario object to a param.net object
resim_nets

Resimulate Dynamic Network at Time 2+
print.netdx

Utility Function for Printing netdx Object
set_current_timestep

Set the Current Timestep
verbose.dcm

Progress Print Module for Deterministic Compartmental Models
toggles_to_diss_stats

Convert Matrix of Toggles to Dissolution and Duration Statistics
summary.netsim

Summary Model Statistics
summary.netest

Summary for Network Model Fit
summary.icm

Summary Model Statistics
recovery.icm.bip

Recovery: icm Module
trim_netest

Function to Reduce the Size of a netest Object
update_unique_ids

Create the Unique Identifiers for New Nodes
prevalence.icm

Get Epidemic Output from icm Model
recovery.icm

Recovery: icm Module
print_nwstats_table

Print Helper For Network Stats Tables
truncate_sim

Truncate Simulation Time Series
test_icm

Test the Model Output from a Stochastic Individual Contact Model
unique_id-tools

Convert Unique Identifiers to/from Positional Identifiers
tedgelist_to_toggles

Convert Timed Edgelist to Matrix of Toggles
verbose.icm

Progress Print Module for Stochastic Individual Contact Models
update_cumulative_edgelist

Update a Cumulative Edgelist of the Specified Network
verbose.net

Progress Print Module for Stochastic Network Models
InitErgmTerm.absdiffnodemix

Definition for absdiffnodemix ERGM Term
InitErgmTerm.fuzzynodematch

Definition for fuzzynodematch ERGM Term
add_vertices

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

Arrivals: netsim Module
apportion_lr

Apportion Using the Largest Remainder Method
EpiModel-package

Mathematical Modeling of Infectious Disease Dynamics
arrivals.icm.bip

Arrivals: Bipartite icm Module
InitErgmTerm.absdiffby

Definition for absdiffby ERGM Term
arrivals.icm

Arrivals: icm Module
arrivals.2g.net

Arrivals: netsim Module