R: Mathematical Modeling of Infectious Disease Dynamics

# Mathematical Modeling of Infectious Disease Dynamics

## Documentation for package ‘EpiModel’ version 2.6.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A C D E F G I M N O P R S T U

EpiModel-package | Mathematical Modeling of Infectious Disease Dynamics

## -- A --

absdiffby | Definition for absdiffby ERGM Term
absdiffnodemix | Definition for absdiffnodemix ERGM Term
add_attr | Functions to Access and Edit the Main netsim_dat Object in Network Models
add_control | Functions to Access and Edit the Main netsim_dat Object in Network Models
add_epi | Functions to Access and Edit the Main netsim_dat Object in Network Models
add_init | Functions to Access and Edit the Main netsim_dat Object in Network Models
add_param | Functions to Access and Edit the Main netsim_dat Object in Network Models
add_vertices | Fast Version of network::add.vertices for Edgelist-formatted Network
append_attr | Functions to Access and Edit the Main netsim_dat Object in Network Models
append_core_attr | Functions to Access and Edit the Main netsim_dat Object in Network Models
apportion_lr | Apportion Using the Largest Remainder Method
arrive_nodes | Arrive New Nodes to the netsim_dat Object
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 for netdx Objects
as.data.frame.netsim | Extract Model Data for Stochastic Models
as.epi.data.frame | Validate and Convert to epi.data.frame
as.network.transmat | Convert transmat Infection Tree into a network Object
as.phylo.transmat | Convert transmat Infection Tree into a phylo Object
as_cumulative_edgelist | Convert an object to a 'cumulative_edgelist'
as_tibble_edgelist | Convert an Edgelist into a Tibble

## -- C --

check_degdist_bal | Check Degree Distribution for Balance in Target Statistics
color_tea | Create 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 netsim_dat Main List Object for a Network Model
create_scenario_list | Make a list of EpiModel scenarios from a data.frame of scenarios

## -- D --

dcm | Deterministic Compartmental Models
dedup_cumulative_edgelist | Deduplicate a cumulative edgelist by combining overlapping edges
delete_edges | Remove Edges That Include Specified Vertices
delete_vertices | Fast Version of network::delete.vertices for Edgelist-formatted Network
depart_nodes | Depart Nodes from the netsim_dat Object
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

## -- F --

fuzzynodematch | Definition for fuzzynodematch ERGM Term

## -- G --

generate_random_params | Generate Values for Random Parameters
geom_bands | ggplot2 Geom for Quantile Bands
get_adj_list | Returns an adjacency list from an edge list
get_attr | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_attr_history | Extract the Attributes History from Network Simulations
get_attr_list | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_backward_reachable | Get the Forward or Backward Reachable Nodes for a Set of Nodes
get_connected_nodes | Returns all the node connected directly or indirectly to a set of nodes
get_control | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_control_list | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_core_attributes | Functions to Access and Edit the Main netsim_dat Object in Network Models
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_cumulative_edgelists_df | Get the Cumulative Edgelists of a Model
get_current_timestep | Return the Current Timestep
get_degree | Get Individual Degree from Network or Edgelist
get_edgelist | Get an Edgelist From the Specified Network
get_edgelists_df | Get the Edgelist(s) from the Specified Network(s)
get_epi | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_epi_list | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_formula_term_attr | Output ERGM Formula Attributes into a Character Vector
get_forward_reachable | Get the Forward or Backward Reachable Nodes for a Set of Nodes
get_init | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_init_list | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_network | Extract Network Objects from Network Simulations
get_network.netdx | Extract Network Objects from Network Simulations
get_network.netsim | Extract Network Objects from Network Simulations
get_network.netsim_dat | Extract Network Objects from Network Simulations
get_network_attributes | Get Network Attributes from a Network Object
get_network_control | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_network_term_attr | Output Network Attributes into a Character Vector
get_nwstats | Extract Network Statistics from netsim or netdx Object
get_param | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_param_list | Functions to Access and Edit the Main netsim_dat Object in Network Models
get_param_set | Extract the Parameter Set from Network Simulations
get_partners | Return the Historical Contacts (Partners) of a Set of Index Nodes
get_posit_ids | Convert Unique Identifiers to/from Positional Identifiers
get_sims | Extract Network Simulations
get_subnet_adj_list | Return an adjacency list of subnets
get_transmat | Extract Transmissions Matrix from Network Epidemic Model
get_unique_ids | Convert Unique Identifiers to/from 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
InitErgmTerm.fuzzynodematch | Definition for fuzzynodematch ERGM Term
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)

## -- M --

make_restart_point | Make a Lightweight Restart Point From a 'netsim' Object with tergmLite
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
multilayer | Specify Controls by Network
mutate_epi | Add New Epidemiology Variables

## -- N --

net-accessor | Functions to Access and Edit the Main netsim_dat Object in Network Models
netdx | Dynamic Network Model Diagnostics
netest | Dynamic Network Model Estimation
netsim | Stochastic Network Models
network_initialize | Initialize Network Object
nwupdate.net | Dynamic Network Updates

## -- O --

overwrite_attrs | Helper to use a 'data.frame' to initialize some attributes

## -- P --

padded_vector | Grow a Vector to a Given Size, Padding it With Empty Elements
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.net_from_table | Parameters List for Stochastic Network Models from a Formatted Data Frame
param.net_to_table | Coerce a list of parameters to a 'long.param.df'
param_random | Create a Value Sampler for Random Parameters
plot.dcm | Plot Data from a Deterministic Compartmental Epidemic Model
plot.epi.data.frame | Plot Epidemic Model Results From a Netsim Data.Frame
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 Three Styles
print.dcm | Print Method for DCM Objects
print.icm | Print Method for ICM Objects
print.netdx | Utility Function for Printing netdx Object
print.netsim | Print Method for Network Model Simulations

## -- R --

reachable-nodes | Get the Forward or Backward Reachable Nodes for a Set of Nodes
record_attr_history | Record Attribute History
record_raw_object | Record an Arbitrary Object During a Simulation
remove_node_attr | Functions to Access and Edit the Main netsim_dat Object in Network Models

## -- S --

set_attr | Functions to Access and Edit the Main netsim_dat Object in Network Models
set_control | Functions to Access and Edit the Main netsim_dat Object in Network Models
set_current_timestep | Set the Current Timestep
set_epi | Functions to Access and Edit the Main netsim_dat Object in Network Models
set_init | Functions to Access and Edit the Main netsim_dat Object in Network Models
set_param | Functions to Access and Edit the Main netsim_dat 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
trim_netest | Function to Reduce the Size of a 'netest' Object
truncate_sim | Truncate Simulation Time Series
truncate_sim.dcm | Truncate Simulation Time Series
truncate_sim.icm | Truncate Simulation Time Series
truncate_sim.netsim | Truncate Simulation Time Series

## -- U --

unique_id-tools | Convert Unique Identifiers to/from Positional Identifiers
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
use_scenario | Apply a scenario object to a param.net object