# Mathematical Modeling of Infectious Disease Dynamics

## Documentation for package ‘EpiModel’ version 2.0.3

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

## Help Pages

EpiModel-package | Mathematical Modeling of Infectious Disease Dynamics
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
append_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.network.transmat | Converts 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
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
dcm | Deterministic Compartmental Models
dissolution_coefs | Dissolution Coefficients for Stochastic Network Models
edgelist_censor | Table of Edge Censoring
EpiModel | Mathematical Modeling of Infectious Disease Dynamics
epiweb | EpiModel Web
geom_bands | ggplot2 geom for Quantile Bands
get_args | Get Arguments from EpiModel Parameterization Functions
get_attr | Functions to Access and Edit the Master List Object in Network Models
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_degree | Get Individual Degree from Network or Edgelist
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_sims | Extract Network Simulations
get_transmat | Extract Transmissions Matrix from Network Epidemic Model
icm | Stochastic Individual Contact Models
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
is.transmat | Extract Transmissions Matrix from Network Epidemic Model
merge.icm | Merge Data across Stochastic Individual Contact Model Simulations
merge.netsim | Merge Model Simulations Across netsim Objects
modules.icm | Modules for Stochastic Individual Contact Models
modules.net | Modules for Stochastic Network Models
mutate_epi | Add New Epidemiology Variables
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
nwupdate.net | Dynamic Network Updates
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
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
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_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
summary.dcm | Summary Model Statistics
summary.icm | Summary Model Statistics
summary.netsim | Summary Model Statistics
transmat | Extract Transmissions Matrix from Network Epidemic Model
truncate_sim | Truncate Simulation Time Series
update_dissolution | Adjust Dissolution Component of Network Model Fit