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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.network(<transmat>)
Convert transmat Infection Tree into a network Object
as.phylo(<transmat>)
Convert transmat Infection Tree into a phylo Object
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
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_attr_history()
Extract the Attributes History from Network Simulations
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
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() 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
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_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 Three Styles
print(<netdx>)
Utility Function for Printing netdx Object
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