Mathematical Modeling of Infectious Disease Dynamics

Documentation for package ‘EpiModel’ version 2.7.0

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Mathematical Modeling of Infectious Disease Dynamics

-- A --

absdiffby	Definition for absdiffby ERGM Term
absdiffnodemix	Definition for absdiffnodemix ERGM Term
add_attr	Get and Set Nodal Attributes in Network Models
add_control	Get and Set Parameters, Controls, and Initial Conditions in Network Models
add_epi	Get and Set Epidemic Outputs in Network Models
add_init	Get and Set Parameters, Controls, and Initial Conditions in Network Models
add_param	Get and Set Parameters, Controls, and Initial Conditions in Network Models
add_vertices	Fast Version of network::add.vertices for Edgelist-formatted Network
append_attr	Get and Set Nodal Attributes in Network Models
append_core_attr	Get and Set Nodal Attributes 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
assign_groups	Assign Group Ids to an Existing Population
as_cumulative_edgelist	Convert an Object to a Cumulative Edgelist
as_tibble_edgelist	Convert an Edgelist into a Tibble

-- B --

by_infection_duration

Parameters That Vary With the Duration of Infection

-- 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
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 --

geom_bands	ggplot2 Geom for Quantile Bands
get_adj_list	Returns an adjacency list from an edge list
get_attr	Get and Set Nodal Attributes in Network Models
get_attr_at	Get Tracked Attributes at a Given Time Step
get_attr_history	Extract the Attributes History from Network Simulations
get_attr_list	Get and Set Nodal Attributes 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	Get and Set Parameters, Controls, and Initial Conditions in Network Models
get_control_list	Get and Set Parameters, Controls, and Initial Conditions in Network Models
get_core_attributes	Get and Set Nodal Attributes 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_degree_dist	Extract Degree Distributions from Network Diagnostics
get_edgelist	Get an Edgelist From the Specified Network
get_edgelists_df	Get the Edgelist(s) from the Specified Network(s)
get_epi	Get and Set Epidemic Outputs in Network Models
get_epi_list	Get and Set Epidemic Outputs 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	Get and Set Parameters, Controls, and Initial Conditions in Network Models
get_init_list	Get and Set Parameters, Controls, and Initial Conditions 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	Get and Set Parameters, Controls, and Initial Conditions 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	Get and Set Parameters, Controls, and Initial Conditions in Network Models
get_param_list	Get and Set Parameters, Controls, and Initial Conditions in Network Models
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_networkDynamic	Build a networkDynamic Object from Simulation Output
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
move_to_group	Move Nodes to Another Group of a Clique Layer
multilayer	Specify Controls and Parameters by Network
mutate_epi	Add New Epidemiology Variables

-- N --

net-accessor	Functions to Access and Edit the Main netsim_dat Object in Network Models
net-controls	Control Settings for Network Model Estimation and Simulation
netcensus	Observed Network Layer for Network Epidemic Models
netclique	Clique Layer for Network Epidemic 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'
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	Get and Set Nodal Attributes in Network Models

-- S --

sample_groups	Sample a Population of Groups from a Table of Group Types
set.control.ergm	Control Settings for Network Model Estimation and Simulation
set.control.ergm.ego	Control Settings for Network Model Estimation and Simulation
set.control.tergm	Control Settings for Network Model Estimation and Simulation
set_attr	Get and Set Nodal Attributes in Network Models
set_control	Get and Set Parameters, Controls, and Initial Conditions in Network Models
set_current_timestep	Set the Current Timestep
set_epi	Get and Set Epidemic Outputs in Network Models
set_init	Get and Set Parameters, Controls, and Initial Conditions in Network Models
set_param	Get and Set Parameters, Controls, and Initial Conditions 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