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EpiModel (version 2.3.2)

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, ).

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Version

Install

install.packages('EpiModel')

Monthly Downloads

933

Version

2.3.2

License

GPL-3

Maintainer

Samuel Jenness

Last Published

February 16th, 2023

Functions in EpiModel (2.3.2)

InitErgmTerm.absdiffnodemix

Definition for absdiffnodemix ERGM Term
EpiModel-package

Mathematical Modeling of Infectious Disease Dynamics
InitErgmTerm.absdiffby

Definition for absdiffby ERGM Term
InitErgmTerm.fuzzynodematch

Definition for fuzzynodematch ERGM Term
arrivals.icm

Arrivals: icm Module
add_vertices

Fast Version of network::add.vertices for Edgelist-formatted Network
arrivals.2g.net

Arrivals: netsim Module
apportion_lr

Apportion Using the Largest Remainder Method
check_degdist_bal

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

Extract Model Data for Deterministic Compartmental Models
check_attr_lengths

Check that All Attributes in the Main Object are of Equal Length
as.phylo.transmat

Convert transmat Infection Tree into a phylo Object
brewer_ramp

RColorBrewer Color Ramp for EpiModel Plots
auto_update_attr

Update Vertex Attributes for Incoming Vertices
as.data.frame.icm

Extract Model Data for Stochastic Models
check_end_horizon_control

Check the format of the end.horizon control
as.network.transmat

Convert transmat Infection Tree into a network Object
as.data.frame.netdx

Extract Timed Edgelists for netdx Objects
arrivals.icm.bip

Arrivals: Bipartite icm Module
create_dat_object

Create a Minimal Main List Object for a Network Model
arrivals.net

Arrivals: netsim Module
create_scenario_list

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

Control Settings for Stochastic Individual Contact Models
control.net

Control Settings for Stochastic Network Models
copy_datattr_to_nwattr

Copy Vertex Attributes from the dat List to the Network Object
copy_nwattr_to_datattr

Copy Vertex Attributes From Network to dat List
color_tea

Create a TEA Variable for Infection Status for ndtv Animations
delete_attr

Delete Elements from Attribute List
comp_plot

Plot Compartment Diagram for Epidemic Models
dcm.mods

Deterministic Compartmental Model Functions
deleteAttr

Delete Elements from Attribute List
crosscheck.dcm

Cross Checking of Inputs for Deterministic Compartmental Models
crosscheck.net

Cross Checking of Inputs for Stochastic Network Models
crosscheck.icm

Cross Checking of Inputs for Stochastic Individual Contact Models
common_updater

Update Either the "param" or "control" List
dcm

Deterministic Compartmental Models
control.dcm

Control Settings for Deterministic Compartmental Models
departures.2g.net

Departures: netsim Module
departures.icm

Departure: icm Module
generate_random_params

Generate Values for Random Parameters
format_param

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

EpiModel Web
get_attr_history

Extract the Attributes History from Network Simulations
delete_vertices

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

Table of Edge Censoring
edges_correct

Adjustment for the Edges Coefficient with Changing Network Size
departures.icm.bip

Departure: Bipartite icm Module
epi_trackers

Function to run the user-provided epi trackers
get_formula_term_attr

Output ERGM Formula Attributes into a Character Vector
get_edgelist

Get an Edgelist From the Specified Network
is.transmat

Extract Transmissions Matrix from Network Epidemic Model
get_current_timestep

Return the Current Timestep
get_degree

Get Individual Degree from Network or Edgelist
get_attr_prop

Proportional Table of Vertex Attributes
get_modules

Get the List of Modules
init.dcm

Initial Conditions for Deterministic Compartmental Models
get_network

Extract networkDynamic and network Objects from Network Simulations
infection.net

Primary Infection Module for netsim
discord_edgelist

Discordant Edgelist
get_network_term_attr

Output Network Attributes into a Character Vector
get_vertex_attribute

Get Vertex Attribute on Network Object
init_status.icm

Disease Status Initialization Module for icm
icm

Stochastic Individual Contact Models
make_stats_table

Create a Summary Table of Simulation Statistics
idgroup

Group Numbers for Two-Group Network
get_param_set

Extract the Parameter Set from Network Simulations
init.icm

Initial Conditions for Stochastic Individual Contact Models
get_nwstats

Extract Network Statistics from netsim or netdx Object
get_nwparam

Extract Network Model Parameters
init_status.net

Disease Status Initialization Module for netsim
departures.net

Departures: netsim Module
init.net

Initial Conditions for Stochastic Network Models
mcat

Write Out Test Progress to Console
geom_bands

ggplot2 Geom for Quantile Bands
get_args

Get Arguments from EpiModel Parameterization Functions
merge.icm

Merge Data across Stochastic Individual Contact Model Simulations
merge.netsim

Merge Model Simulations across netsim Objects
mutate_epi

Add New Epidemiology Variables
get_partners

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

Extract Network Simulations
increment_timestep

Increment the Current Timestep
infection.2g.net

Primary Infection Module for netsim
init_tergmLite

Initialize EpiModel netsim Object for tergmLite Simulation
dissolution_coefs

Dissolution Coefficients for Stochastic Network Models
initialize.icm

Initialization: icm Module
net-accessor

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

Get a Cumulative Edgelist From a Specified Network
nwupdate.net

Dynamic Network Updates
netsim

Stochastic Network Models
get_cumulative_edgelists_df

Get the Cumulative Edgelists of a Model
infection.icm

Primary Infection Module for icm
netsim_error_logger

Handle the Logging of Traceback and Dumping of Frames on Error
is_active_unique_ids

Are These Nodes Active (Unique IDs)
infection.icm.bip

Primary Infection Module for icm
network_initialize

Initialize Network Object
prevalence.icm.bip

Get Epidemic Output from icm Model
plot.dcm

Plot Data from a Deterministic Compartmental Epidemic Model
prevalence.net

Get Epidemic Output from netsim Model
netdx

Dynamic Network Model Diagnostics
make_module_list

Populate the Module List After the Initialization Module is run
netest

Dynamic Network Model Estimation
netsim_cond_msg

Message to Find in Which Module a condition Occurred
plot.icm

Plot Data from a Stochastic Individual Contact Epidemic Model
param.icm

Epidemic Parameters for Stochastic Individual Contact Models
record_attr_history

Record Attribute History
param.dcm

Epidemic Parameters for Deterministic Compartmental Models
param.net

Epidemic Parameters for Stochastic Network Models
recovery.net

Recovery: netsim Module
process_out.net

Save a List of netsim Data to Output List Format
print.netdx

Utility Function for Printing netdx Object
summary.netsim

Summary Model Statistics
tedgelist_to_toggles

Convert Timed Edgelist to Matrix of Toggles
reexports

Objects exported from other packages
plot.netdx

Plot Dynamic Network Model Diagnostics
plot.netsim

Plot Data from a Stochastic Network Epidemic Model
update_params

Update Model Parameters for Stochastic Network Models
recovery.icm

Recovery: icm Module
recovery.icm.bip

Recovery: icm Module
is_active_posit_ids

Are These Nodes Active (Positional IDs)
initialize.net

Initialization: netsim Module
update_unique_ids

Create the Unique Identifiers for New Nodes
set_transmat

Save Transmission Matrix
recovery.2g.net

Recovery: netsim Module
record_raw_object

Record an Arbitrary Object During a Simulation
modules.icm

Modules for Stochastic Individual Contact Models
modules.net

Modules for Stochastic Network Models
param_random

Create a Value Sampler for Random Parameters
toggles_to_diss_stats

Convert Matrix of Toggles to Dissolution and Duration Statistics
set_modules

Set the List of Modules
param.net_from_table

Parameters List for Stochastic Network Models from a Formatted Data Frame
print_nwstats_table

Print Helper For Network Stats Tables
summary.icm

Summary Model Statistics
trigger_end_horizon

Function to Trigger the End Horizon
set_vertex_attribute

Set Vertex Attribute on Network Object
unique_id-tools

Convert Unique Identifiers to/from Positional Identifiers
summary.netest

Summary for Network Model Fit
update_dissolution

Adjust Dissolution Component of Network Model Fit
update_list

Update List x Using the Elements of List new.x.
sim_nets_t1

Simulate Initial Network at Time 1 for Model Initialization
update_cumulative_edgelist

Update a Cumulative Edgelist of the Specified Network
plot.transmat

Plot transmat Infection Tree in Three Styles
verbose.icm

Progress Print Module for Stochastic Individual Contact Models
verbose.net

Progress Print Module for Stochastic Network Models
saveout.dcm

Save dcm Data to Output List Format
saveout.icm

Save icm Data to Output List Format
prevalence.icm

Get Epidemic Output from icm Model
remove_modules

Remove a Set of Modules From the Module List
set_current_timestep

Set the Current Timestep
saveout.net

Save netsim Data to Output List Format
test_icm

Test the Model Output from a Stochastic Individual Contact Model
ssample

Stable Sampling Function
test_net

Test the Model Output from a Network Model
summary.dcm

Summary Model Statistics
trim_netest

Function to Reduce the Size of a netest Object
resim_nets

Resimulate Dynamic Network at Time 2+
truncate_sim

Truncate Simulation Time Series
use_scenario

Apply a scenario object to a param.net object
verbose.dcm

Progress Print Module for Deterministic Compartmental Models