# Mathematical Modeling of Infectious Disease Dynamics

## Documentation for package ‘EpiModel’ version 2.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D E G I L M N P R S T U misc

EpiModel-package | Mathematical Modeling of Infectious Disease Dynamics

## -- A --

absdiffby | Definition for absdiffby ERGM Term
absdiffnodemix | Definition for absdiffnodemix ERGM Term
add.edges.networkLite | networkLite Methods
add_attr | Functions to Access and Edit the Master List Object in Network Models
add_control | Functions to Access and Edit the Master List Object in Network Models
add_epi | Functions to Access and Edit the Master List Object in Network Models
add_init | Functions to Access and Edit the Master List Object in Network Models
add_param | Functions to Access and Edit the Master List Object in Network Models
add_vertices | Fast Version of network::add.vertices for Edgelist-formated Network
append_attr | Functions to Access and Edit the Master List Object in Network Models
append_core_attr | Functions to Access and Edit the Master List Object in Network Models
apportion_lr | Apportion Least-Remainder Method
as.data.frame.dcm | Extract Model Data for Deterministic Compartmental Models
as.data.frame.icm | Extract Model Data for Stochastic Models
as.data.frame.netdx | Extract Timed Edgelists netdx Objects
as.data.frame.netsim | Extract Model Data for Stochastic Models
as.edgelist.networkLite | networkLite Methods
as.network.transmat | Converts transmat infection tree into a network object
as.networkLite | networkLite Methods
as.networkLite.network | networkLite Methods
as.networkLite.networkLite | networkLite Methods
as.phylo.transmat | Convert transmat infection tree into a phylo object

## -- C --

check_degdist_bal | Check Degree Distribution for Balance in Target Statistics
color_tea | Creates a TEA Variable for Infection Status for 'ndtv' Animations
comp_plot | Plot Compartment Diagram for Epidemic Models
comp_plot.dcm | Plot Compartment Diagram for Epidemic Models
comp_plot.icm | Plot Compartment Diagram for Epidemic Models
comp_plot.netsim | Plot Compartment Diagram for Epidemic Models
control.dcm | Control Settings for Deterministic Compartmental Models
control.icm | Control Settings for Stochastic Individual Contact Models
control.net | Control Settings for Stochastic Network Models
create_dat_object | Create a Minimal Master List Object of Network Model

## -- D --

dcm | Deterministic Compartmental Models
delete_vertices | Fast Version of network::delete.vertices for Edgelist-formated Network
dissolution_coefs | Dissolution Coefficients for Stochastic Network Models

## -- E --

edgelist_censor | Table of Edge Censoring
EpiModel | Mathematical Modeling of Infectious Disease Dynamics
epiweb | EpiModel Web

## -- G --

generate_random_params | Generate Values for Random Parameters
geom_bands | ggplot2 geom for Quantile Bands
get.network.attribute.networkLite | networkLite Methods
get.vertex.attribute.networkLite | networkLite Methods
get_args | Get Arguments from EpiModel Parameterization Functions
get_attr | Functions to Access and Edit the Master List Object in Network Models
get_attr_history | Extract the Attributes History from Network Simulations
get_attr_list | Functions to Access and Edit the Master List Object in Network Models
get_control | Functions to Access and Edit the Master List Object in Network Models
get_control_list | Functions to Access and Edit the Master List Object in Network Models
get_cumulative_edgelist | Get a Cumulative Edgelist From a Specified Network
get_cumulative_edgelists_df | Get the Cumulative Edgelists of a Model
get_current_timestep | Returns the Current Timestep
get_degree | Get Individual Degree from Network or Edgelist
get_edgelist | Get an Edgelist From the Specified Network
get_epi | Functions to Access and Edit the Master List Object in Network Models
get_epi_list | Functions to Access and Edit the Master List Object in Network Models
get_formula_term_attr | Outputs ERGM Formula Attributes into a Character Vector
get_init | Functions to Access and Edit the Master List Object in Network Models
get_init_list | Functions to Access and Edit the Master List Object in Network Models
get_network | Extract networkDynamic and network Objects from Network Simulations
get_network_term_attr | Outputs ERGM Formula Attributes into a Character Vector
get_nwstats | Extract Network Statistics from netsim or netdx Object
get_param | Functions to Access and Edit the Master List Object in Network Models
get_param_list | Functions to Access and Edit the Master List Object in Network Models
get_param_set | Extract the Parameter Set from Network Simulations
get_partners | Return the Historical Partners (Contacts) of a Set of Index Patients
get_posit_ids | Convert Unique identifiers from/to Positional identifiers
get_sims | Extract Network Simulations
get_transmat | Extract Transmissions Matrix from Network Epidemic Model
get_unique_ids | Convert Unique identifiers from/to Positional identifiers
get_vertex_attribute | Get Vertex Attribute on Network Object

## -- I --

icm | Stochastic Individual Contact Models
increment_timestep | Increment the Current Timestep
init.dcm | Initial Conditions for Deterministic Compartmental Models
init.icm | Initial Conditions for Stochastic Individual Contact Models
init.net | Initial Conditions for Stochastic Network Models
InitErgmTerm.absdiffby | Definition for absdiffby ERGM Term
InitErgmTerm.absdiffnodemix | Definition for absdiffnodemix ERGM Term
init_tergmLite | Initializes EpiModel netsim Object for tergmLite Simulation
is.transmat | Extract Transmissions Matrix from Network Epidemic Model
is_active_posit_ids | Are These Nodes Active (Positional IDs)
is_active_unique_ids | Are These Nodes Active (Unique IDs)

## -- L --

list.network.attributes.networkLite | networkLite Methods
list.vertex.attributes.networkLite | networkLite Methods

## -- M --

merge.icm | Merge Data across Stochastic Individual Contact Model Simulations
merge.netsim | Merge Model Simulations Across netsim Objects
mixingmatrix.networkLite | networkLite Methods
modules.icm | Modules for Stochastic Individual Contact Models
modules.net | Modules for Stochastic Network Models
mutate_epi | Add New Epidemiology Variables

## -- N --

net-accessor | Functions to Access and Edit the Master List Object in Network Models
netdx | Dynamic Network Model Diagnostics
netest | Dynamic Network Model Estimation
netsim | Stochastic Network Models
network.edgecount.networkLite | networkLite Methods
network.naedgecount.networkLite | networkLite Methods
networkLite | networkLite Constructor Utilities
networkLite.edgelist | networkLite Constructor Utilities
networkLite.matrix | networkLite Constructor Utilities
networkLite.numeric | networkLite Constructor Utilities
networkLitemethods | networkLite Methods
network_initialize | Initialize Network Object
nwupdate.net | Dynamic Network Updates

## -- P --

param.dcm | Epidemic Parameters for Deterministic Compartmental Models
param.icm | Epidemic Parameters for Stochastic Individual Contact Models
param.net | Epidemic Parameters for Stochastic Network Models
param_random | Create a Value Sampler for Random Parameters
plot.dcm | Plot Data from a Deterministic Compartmental Epidemic Model
plot.icm | Plot Data from a Stochastic Individual Contact Epidemic Model
plot.netdx | Plot Dynamic Network Model Diagnostics
plot.netsim | Plot Data from a Stochastic Network Epidemic Model
plot.transmat | Plot transmat infection tree in one of several styles
print.networkLite | networkLite Methods

## -- R --

record_attr_history | Record Attributes History
record_raw_object | Record an Arbitrary Object During a Simulation

## -- S --

set.network.attribute.networkLite | networkLite Methods
set.vertex.attribute.networkLite | networkLite Methods
set_attr | Functions to Access and Edit the Master List Object in Network Models
set_control | Functions to Access and Edit the Master List Object in Network Models
set_current_timestep | Sets the Current Timestep
set_epi | Functions to Access and Edit the Master List Object in Network Models
set_init | Functions to Access and Edit the Master List Object in Network Models
set_param | Functions to Access and Edit the Master List Object in Network Models
set_transmat | Save Transmission Matrix
set_vertex_attribute | Set Vertex Attribute on Network Object
summary.dcm | Summary Model Statistics
summary.icm | Summary Model Statistics
summary.netsim | Summary Model Statistics

## -- T --

transmat | Extract Transmissions Matrix from Network Epidemic Model
truncate_sim | Truncate Simulation Time Series

## -- U --

unique_id-tools | Convert Unique identifiers from/to Positional identifiers
updater.net | Module to modify the controls or parameters during the simulation
update_cumulative_edgelist | Update a Cumulative Edgelist of the Specified Network
update_dissolution | Adjust Dissolution Component of Network Model Fit
update_params | Update Model Parameters for Stochastic Network Models

## -- misc --

[<-.networkLite | networkLite Methods