Package index • EpiModel

All functions

EpiModel-package EpiModel: Mathematical Modeling of Infectious Disease Dynamics

InitErgmTerm.absdiffby(): Definition for absdiffby ERGM Term

InitErgmTerm.absdiffnodemix(): Definition for absdiffnodemix ERGM Term

InitErgmTerm.fuzzynodematch(): Definition for fuzzynodematch ERGM Term

add_vertices(): Fast Version of network::add.vertices for Edgelist-formatted Network

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>) as.data.frame(<netsim>): Extract Model Data for Stochastic Models

as.data.frame(<netdx>): Extract Timed Edgelists for netdx Objects

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

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

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

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

edgelist_censor(): Table of Edge Censoring

epiweb(): EpiModel Web

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_history(): Extract the Attributes History from Network Simulations

get_connected_nodes(): Returns all the node connected directly or indirectly to a set of nodes

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_formula_term_attr(): Output ERGM Formula Attributes into a Character Vector

get_network(): Extract Network Objects from Network Simulations

get_network_attributes(): Get Network Attributes from a Network Object

get_network_term_attr(): Output Network Attributes into a Character Vector

get_nwstats(): Extract Network Statistics from netsim or netdx Object

get_param_set(): Extract the Parameter Set from Network Simulations

get_partners(): Return the Historical Contacts (Partners) of a Set of Index Nodes

get_sims(): Extract Network Simulations

get_subnet_adj_list(): Return an adjacency list of subnets

is.transmat() get_transmat(): Extract Transmissions Matrix from Network Epidemic Model

get_vertex_attribute(): Get Vertex Attribute on Network Object

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

is_active_posit_ids(): Are These Nodes Active (Positional IDs)

is_active_unique_ids(): Are These Nodes Active (Unique IDs)

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

get_attr_list() get_attr() add_attr() set_attr() append_attr() remove_node_attr() get_epi_list() get_epi() add_epi() set_epi() get_param_list() get_param() add_param() set_param() get_control_list() get_control() get_network_control() add_control() set_control() get_init_list() get_init() add_init() set_init() append_core_attr(): 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

overwrite_attrs(): Helper to use a data.frame to initialize some attributes

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(<netdx>): Utility Function for Printing netdx Object

get_forward_reachable() get_backward_reachable(): 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

set_current_timestep(): Set the Current Timestep

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

trim_netest(): Function to Reduce the Size of a netest Object

truncate_sim(): Truncate Simulation Time Series

get_unique_ids() get_posit_ids(): 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