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EpiModel (version 2.5.0)

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

820

Version

2.5.0

License

GPL-3

Maintainer

Samuel Jenness

Last Published

October 11th, 2024

Functions in EpiModel (2.5.0)

InitErgmTerm.absdiffnodemix

Definition for absdiffnodemix ERGM Term
arrivals.icm.bip

Arrivals: Bipartite icm Module
arrivals.2g.net

Arrivals: netsim Module
InitErgmTerm.fuzzynodematch

Definition for fuzzynodematch ERGM Term
arrivals.icm

Arrivals: icm Module
as.epi.data.frame

Validate and Convert to epi.data.frame
as_tibble_edgelist

Convert an Edgelist into a Tibble
as.phylo.transmat

Convert transmat Infection Tree into a phylo Object
add_vertices

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

Update Vertex Attributes for Incoming Vertices
as_cumulative_edgelist

Convert an object to a cumulative_edgelist
arrivals.net

Arrivals: netsim Module
apportion_lr

Apportion Using the Largest Remainder Method
check_degdist_bal

Check Degree Distribution for Balance in Target Statistics
check_end_horizon_control

Check the format of the end.horizon control
control.icm

Control Settings for Stochastic Individual Contact Models
crosscheck.dcm

Cross Checking of Inputs for Deterministic Compartmental Models
crosscheck.icm

Cross Checking of Inputs for Stochastic Individual Contact Models
as.network.transmat

Convert transmat Infection Tree into a network Object
color_tea

Create a TEA Variable for Infection Status for ndtv Animations
control.net

Control Settings for Stochastic Network Models
common_updater

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

Plot Compartment Diagram for Epidemic Models
dcm

Deterministic Compartmental Models
crosscheck.net

Cross Checking of Inputs for Stochastic Network Models
delete_vertices

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

Deterministic Compartmental Model Functions
control.dcm

Control Settings for Deterministic Compartmental Models
EpiModel-package

Mathematical Modeling of Infectious Disease Dynamics
copy_datattr_to_nwattr

Copy Vertex Attributes from the netsim_dat List to the Network Objects
depart_nodes

Depart Nodes from the netsim_dat Object
dedup_cumulative_edgelist

Deduplicate a cumulative edgelist by combining overlapping edges
copy_nwattr_to_datattr

Copy Vertex Attributes From Network to netsim_dat List
discord_edgelist

Discordant Edgelist
get_degree

Get Individual Degree from Network or Edgelist
arrive_nodes

Arrive New Nodes to the netsim_dat Object
InitErgmTerm.absdiffby

Definition for absdiffby ERGM Term
as.data.frame.dcm

Extract Model Data for Deterministic Compartmental Models
departures.icm.bip

Departure: Bipartite icm Module
get_discordant_edgelist

Get Discordant Edgelist Based on Specified Status Variable
create_dat_object

Create a Minimal netsim_dat Main List Object for a Network Model
departures.net

Departures: netsim Module
dissolution_coefs

Dissolution Coefficients for Stochastic Network Models
as.data.frame.icm

Extract Model Data for Stochastic Models
delete_attr

Delete Elements from Attribute List
get_args

Get Arguments from EpiModel Parameterization Functions
create_scenario_list

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

Remove Edges That Include Specified Vertices
geom_bands

ggplot2 Geom for Quantile Bands
get_attr_history

Extract the Attributes History from Network Simulations
idgroup

Group Numbers for Two-Group Network
departures.2g.net

Departures: netsim Module
departures.icm

Departure: icm Module
get_attr_prop

Proportional Table of Vertex Attributes
as.data.frame.netdx

Extract Timed Edgelists for netdx Objects
format_param

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

Generate Values for Random Parameters
get_connected_nodes

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

Increment the Current Timestep
get_formula_term_attr

Output ERGM Formula Attributes into a Character Vector
get_nwstats

Extract Network Statistics from netsim or netdx Object
get_modules

Get the List of Modules
brewer_ramp

RColorBrewer Color Ramp for EpiModel Plots
edgelist_censor

Table of Edge Censoring
check_attr_lengths

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

Adjustment for the Edges Coefficient with Changing Network Size
init.dcm

Initial Conditions for Deterministic Compartmental Models
get_adj_list

Returns an adjacency list from an edge list
get_cumulative_edgelists_df

Get the Cumulative Edgelists of a Model
epi_trackers

Function to run the user-provided epi trackers
epiweb

EpiModel Web
get_cumulative_degree

Return the Cumulative Degree of a Set of Index Nodes
get_cumulative_edgelist

Get a Cumulative Edgelist From a Specified Network
get_param_set

Extract the Parameter Set from Network Simulations
infection.icm.bip

Primary Infection Module for icm
init.icm

Initial Conditions for Stochastic Individual Contact Models
get_edgelist

Get an Edgelist From the Specified Network
infection.net

Primary Infection Module for netsim
multilayer

Specify Controls by Network
modules.net

Modules for Stochastic Network Models
get_network_term_attr

Output Network Attributes into a Character Vector
get_vertex_attribute

Get Vertex Attribute on Network Object
get_nwparam

Extract Network Model Parameters
icm

Stochastic Individual Contact Models
get_current_timestep

Return the Current Timestep
get_edgelists_df

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

Write Out Test Progress to Console
merge.icm

Merge Data across Stochastic Individual Contact Model Simulations
get_network

Extract Network Objects from Network Simulations
get_subnet_adj_list

Return an adjacency list of subnets
get_partners

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

Get Network Attributes from a Network Object
netsim_error_logger

Handle the Logging of Traceback and Dumping of Frames on Error
is.transmat

Extract Transmissions Matrix from Network Epidemic Model
padded_vector

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

Initial Conditions for Stochastic Network Models
initialize.icm

Initialization: icm Module
get_sims

Extract Network Simulations
infection.2g.net

Primary Infection Module for netsim
init_nets

Network Data and Stats Initialization
network_initialize

Initialize Network Object
initialize.net

Initialization: netsim Module
is_active_posit_ids

Are These Nodes Active (Positional IDs)
nwupdate.net

Dynamic Network Updates
param.dcm

Epidemic Parameters for Deterministic Compartmental Models
plot.epi.data.frame

Plot Epidemic Model Results From a Netsim Data.Frame
mutate_epi

Add New Epidemiology Variables
param.net_from_table

Parameters List for Stochastic Network Models from a Formatted Data Frame
net-accessor

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

Plot Data from a Stochastic Individual Contact Epidemic Model
print.netdx

Utility Function for Printing netdx Object
netsim

Stochastic Network Models
netsim_cond_msg

Message to Find in Which Module a condition Occurred
print_nwstats_table

Print Helper For Network Stats Tables
set_modules

Set the List of Modules
infection.icm

Primary Infection Module for icm
set_network

Set Network State During netsim Simulation
overwrite_attrs

Helper to use a data.frame to initialize some attributes
param_random

Create a Value Sampler for Random Parameters
param.net_to_table

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

Record Attribute History
init_status.icm

Disease Status Initialization Module for icm
is_active_unique_ids

Are These Nodes Active (Unique IDs)
trigger_end_horizon

Function to Trigger the End Horizon
init_status.net

Disease Status Initialization Module for netsim
record_raw_object

Record an Arbitrary Object During a Simulation
param.icm

Epidemic Parameters for Stochastic Individual Contact Models
make_module_list

Populate the Module List After the Initialization Module is run
recovery.icm.bip

Recovery: icm Module
param.net

Epidemic Parameters for Stochastic Network Models
recovery.net

Recovery: netsim Module
make_stats_table

Create a Summary Table of Simulation Statistics
netdx

Dynamic Network Model Diagnostics
plot.transmat

Plot transmat Infection Tree in Three Styles
modules.icm

Modules for Stochastic Individual Contact Models
merge.netsim

Merge Model Simulations across netsim Objects
prevalence.icm

Get Epidemic Output from icm Model
trim_netest

Function to Reduce the Size of a netest Object
sim_nets_t1

Initialize Networks Used in netsim
netest

Dynamic Network Model Estimation
remove_modules

Remove a Set of Modules From the Module List
update_cumulative_edgelist

Update a Cumulative Edgelist of the Specified Network
resim_nets

Resimulate Dynamic Network at Time 2+
update_dissolution

Adjust Dissolution Component of Network Model Fit
recovery.2g.net

Recovery: netsim Module
simulate_dat

Simulate a Network for a Specified Number of Time Steps
truncate_sim

Truncate Simulation Time Series
plot.netdx

Plot Dynamic Network Model Diagnostics
set_transmat

Save Transmission Matrix
plot.netsim

Plot Data from a Stochastic Network Epidemic Model
set_vertex_attribute

Set Vertex Attribute on Network Object
test_net

Test the Model Output from a Network Model
plot.dcm

Plot Data from a Deterministic Compartmental Epidemic Model
toggles_to_diss_stats

Convert Matrix of Toggles to Dissolution and Duration Statistics
prevalence.icm.bip

Get Epidemic Output from icm Model
process_out.net

Save a List of netsim Data to Output List Format
update_list

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

Recovery: icm Module
unique_id-tools

Convert Unique Identifiers to/from Positional Identifiers
update_unique_ids

Create the Unique Identifiers for New Nodes
prevalence.net

Get Epidemic Output from netsim Model
update_params

Update Model Parameters for Stochastic Network Models
reachable-nodes

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

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

Save dcm Data to Output List Format
saveout.net

Save netsim Data to Output List Format
set_current_timestep

Set the Current Timestep
saveout.icm

Save icm Data to Output List Format
summary.dcm

Summary Model Statistics
ssample

Stable Sampling Function
summary.netsim

Summary Model Statistics
summary.icm

Summary Model Statistics
verbose.dcm

Progress Print Module for Deterministic Compartmental Models
summary_nets

Extract Summary Statistics of Networks Used in netsim
summary.netest

Summary for Network Model Fit
verbose.icm

Progress Print Module for Stochastic Individual Contact Models
tedgelist_to_toggles

Convert Timed Edgelist to Matrix of Toggles
test_icm

Test the Model Output from a Stochastic Individual Contact Model
verbose.net

Progress Print Module for Stochastic Network Models