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EpiModel (version 2.2.0)

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

838

Version

2.2.0

License

GPL-3

Maintainer

Samuel Jenness

Last Published

November 9th, 2021

Functions in EpiModel (2.2.0)

apportion_lr

Apportion Least-Remainder Method
check_attr_lengths

Check that all attributes in the master object are of equal length
EpiModel-package

Mathematical Modeling of Infectious Disease Dynamics
InitErgmTerm.absdiffby

Definition for absdiffby ERGM Term
InitErgmTerm.absdiffnodemix

Definition for absdiffnodemix ERGM Term
add_vertices

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

Updates Vertex Attributes for Incoming Vertices
control.net

Control Settings for Stochastic Network Models
copy_datattr_to_nwattr

Copies Vertex Attributes from the dat List to the Network Object
check_degdist_bal

Check Degree Distribution for Balance in Target Statistics
departures.icm.bip

Departure: bipartite icm Module
brewer_ramp

RColorBrewer Color Ramp for EpiModel Plots
discord_edgelist

Discordant Edgelist
control.dcm

Control Settings for Deterministic Compartmental Models
departures.net

Departures: netsim Module
as.network.transmat

Converts transmat infection tree into a network object
dissolution_coefs

Dissolution Coefficients for Stochastic Network Models
geom_bands

ggplot2 geom for Quantile Bands
get_sims

Extract Network Simulations
get_cumulative_edgelists_df

Get the Cumulative Edgelists of a Model in data.frame Format
get_cumulative_edgelist

Get a Cumulative Edgelist From the Specified Network
get_args

Get Arguments from EpiModel Parameterization Functions
is.transmat

Extract Transmissions Matrix from Network Epidemic Model
control.icm

Control Settings for Stochastic Individual Contact Models
infection.icm.bip

Primary Infection Module for icm
infection.net

Primary Infection Module for netsim
edges_correct

Adjustment for the Edges Coefficient with Changing Network Size
modules.icm

Modules for Stochastic Individual Contact Models
networkLite

networkLite Constructor Utilities
merge.netsim

Merge Model Simulations Across netsim Objects
networkLitemethods

networkLite Methods
plot.netsim

Plot Data from a Stochastic Network Epidemic Model
plot.netdx

Plot Dynamic Network Model Diagnostics
format_param

Format one parameter for printing with the `print.param.xxx` functions
generate_random_params

Generate Values for Random Parameters
dcm.mods

Deterministic Compartmental Model Functions
as.phylo.transmat

Convert transmat infection tree into a phylo object
dcm

Deterministic Compartmental Models
crosscheck.net

Cross Checking of Inputs for Stochastic Network Models
resim_nets

Resimulate Dynamic Network at Time 2+
saveout.dcm

Save dcm Data to Output List Format
edgelist_censor

Table of Edge Censoring
epiweb

EpiModel Web
deleteAttr

Delete Elements from Attribute List
edgelist_meanage

Mean Age of Partnerships over Time
get_edgelist

Get an Edgelist From the Specified Network
get_nwparam

Extract Network Model Parameters
get_current_timestep

Returns the Current Timestep
get_nwstats

Extract Network Statistics from netsim or netdx Object
get_formula_term_attr

Outputs ERGM Formula Attributes into a Character Vector
get_vertex_attribute

Get Vertex Attribute on Network Object
icm

Stochastic Individual Contact Models
make_formation_table

Calculate the Formation Statistics of a Network
network_initialize

Initialize Network Object
make_dissolution_stats

Calculate the Dissolution Statistics of a Network
initialize.icm

Initialization: icm Module
get_degree

Get Individual Degree from Network or Edgelist
get_param_set

Extract the Parameter Set from Network Simulations
get_partners

Get the Previous Partners of a Set of Indexes
summary.icm

Summary Model Statistics
summary.dcm

Summary Model Statistics
nwupdate.net

Dynamic Network Updates
as.data.frame.dcm

Extract Model Data for Deterministic Compartmental Models
arrivals.net

Arrivals: netsim Module
init_tergmLite

Initializes EpiModel netsim Object for tergmLite Simulation
initialize.net

Initialization: netsim Module
modules.net

Modules for Stochastic Network Models
init_status.net

Disease Status Initialization Module for netsim
is_active_unique_ids

Are These Nodes Active (Unique IDs)
is_active_posit_ids

Are These Nodes Active (Positional IDs)
mutate_epi

Add New Epidemiology Variables
netest

Dynamic Network Model Estimation
plot.dcm

Plot Data from a Deterministic Compartmental Epidemic Model
netsim

Stochastic Network Models
netsim_cond_msg

Message to find in which module a `condition` occured
plot.icm

Plot Data from a Stochastic Individual Contact Epidemic Model
recovery.2g.net

Recovery: netsim Module
color_tea

Creates a TEA Variable for Infection Status for ndtv Animations
recovery.icm

Recovery: icm Module
comp_plot

Plot Compartment Diagram for Epidemic Models
crosscheck.icm

Cross Checking of Inputs for Stochastic Individual Contact Models
crosscheck.dcm

Cross Checking of Inputs for Deterministic Compartmental Models
netsim_loop

Internal function running the network simulation loop
departures.2g.net

Departures: netsim Module
param.net

Epidemic Parameters for Stochastic Network Models
update_params

Update Model Parameters for Stochastic Network Models
set_vertex_attribute

Set Vertex Attribute on Network Object
print_nwstats_table

Print Helper For Network Stats Tables
update_unique_ids

Create the unique_ids for the new nodes
sim_nets_t1

Simulate Initial Network at Time 1 for Model Initialization
process_out.net

Save a list of netsim Data to Output List Format
departures.icm

Departure: icm Module
truncate_sim

Truncate Simulation Time Series
snctrl

Statnet Control
updater.net

Module to modify the parameters during the simulation
ssample

Stable Sampling Function
trackers.net

Trackers: netsim Module
verbose.dcm

Progress Print Module for Deterministic Compartmental Models
arrivals.icm

Arrivals: icm Module
idgroup

Mode Numbers for Two-Group Network
arrivals.icm.bip

Arrivals: bipartite icm Module
create_dat_object

Create a Minimal Master List Object of Network Model
as.data.frame.netdx

Extract Timed Edgelists netdx Objects
delete_vertices

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

Delete Elements from Attribute List
as.data.frame.icm

Extract Model Data for Stochastic Models
copy_nwattr_to_datattr

Copies Vertex Attributes From Network to dat List
param_random

Create a Value Sampler for Random Parameters
record_raw_object

Record an Arbitrary Object During a Simulation
record_attr_history

Record Attributes History
update_dissolution

Adjust Dissolution Component of Network Model Fit
increment_timestep

Increment the Current Timestep
test_net

Test the Model Output from a Network Model
init.dcm

Initial Conditions for Deterministic Compartmental Models
test_icm

Test the Model Output from a Stochastic Individual Contact Model
update_list

Update list x using the elements of list new.x.
init.icm

Initial Conditions for Stochastic Individual Contact Models
get_attr_history

Extract the Attributes History from Network Simulations
get_network

Extract networkDynamic and network Objects from Network Simulations
get_network_term_attr

Outputs ERGM Formula Attributes into a Character Vector
param.dcm

Epidemic Parameters for Deterministic Compartmental Models
infection.2g.net

Primary Infection Module for netsim
get_attr_prop

Proportional Table of Vertex Attributes
infection.icm

Primary Infection Module for icm
recovery.icm.bip

Recovery: icm Module
param.icm

Epidemic Parameters for Stochastic Individual Contact Models
init.net

Initial Conditions for Stochastic Network Models
recovery.net

Recovery: netsim Module
saveout.icm

Save icm Data to Output List Format
saveout.net

Save netsim Data to Output List Format
init_status.icm

Disease Status Initialization Module for icm
update_cumulative_edgelist

Update a Cumulative Edgelist of the Specified Network
unique_id-tools

Convert Unique identifiers from/to Positional identifiers
verbose.icm

Progress Print Module for Stochastic Individual Contact Models
verbose.net

Progress Print Module for Stochastic Network Models
mcat

Write Out Test Progress to Console
merge.icm

Merge Data across Stochastic Individual Contact Model Simulations
net-accessor

Functions to Access and Edit the Master List Object in Network Models
netdx

Dynamic Network Model Diagnostics
plot.transmat

Plot transmat infection tree in one of several styles
prevalence.icm.bip

Get Epidemic Output from icm Model
prevalence.icm

Get Epidemic Output from icm Model
prevalence.net

Get Epidemic Output from netsim Model
set_current_timestep

Sets the Current Timestep
summary.netest

Summary for Network Model Fit
set_transmat

Save Transmission Matrix
summary.netsim

Summary Model Statistics
arrivals.2g.net

Arrivals: netsim Module