Man pages for EpiModel
Mathematical Modeling of Infectious Disease Dynamics

add_verticesFast Version of network::add.vertices for Edgelist-formatted...
apportion_lrApportion Using the Largest Remainder Method
arrivals.2g.netArrivals: netsim Module
arrivals.icmArrivals: icm Module
arrivals.icm.bipArrivals: Bipartite icm Module
arrivals.netArrivals: netsim Module
arrive_nodesArrive New Nodes to the netsim_dat Object Model Data for Deterministic Compartmental Models Model Data for Stochastic Models Timed Edgelists for netdx Objects transmat Infection Tree into a network Object
as.phylo.transmatConvert transmat Infection Tree into a phylo Object
auto_update_attrUpdate Vertex Attributes for Incoming Vertices
brewer_rampRColorBrewer Color Ramp for EpiModel Plots
check_attr_lengthsCheck that All Attributes in the Main 'netsim_dat' Object are...
check_degdist_balCheck Degree Distribution for Balance in Target Statistics
check_end_horizon_controlCheck the format of the end.horizon control
color_teaCreate a TEA Variable for Infection Status for 'ndtv'...
common_updaterUpdate Either the "param" or "control" List
comp_plotPlot Compartment Diagram for Epidemic Models
control.dcmControl Settings for Deterministic Compartmental Models
control.icmControl Settings for Stochastic Individual Contact Models
control.netControl Settings for Stochastic Network Models
copy_datattr_to_nwattrCopy Vertex Attributes from the 'netsim_dat' List to the...
copy_nwattr_to_datattrCopy Vertex Attributes From Network to 'netsim_dat' List
create_dat_objectCreate a Minimal netsim_dat Main List Object for a Network...
create_scenario_listMake a list of EpiModel scenarios from a data.frame of...
crosscheck.dcmCross Checking of Inputs for Deterministic Compartmental...
crosscheck.icmCross Checking of Inputs for Stochastic Individual Contact...
crosscheck.netCross Checking of Inputs for Stochastic Network Models
dcmDeterministic Compartmental Models
dcm.modsDeterministic Compartmental Model Functions
delete_attrDelete Elements from Attribute List
deleteAttrDelete Elements from Attribute List
delete_edgesRemove Edges That Include Specified Vertices
delete_verticesFast Version of network::delete.vertices for...
depart_nodesDepart Nodes from the netsim_dat Object
departures.2g.netDepartures: netsim Module
departures.icmDeparture: icm Module
departures.icm.bipDeparture: Bipartite icm Module
departures.netDepartures: netsim Module
discord_edgelistDiscordant Edgelist
dissolution_coefsDissolution Coefficients for Stochastic Network Models
edgelist_censorTable of Edge Censoring
edges_correctAdjustment for the Edges Coefficient with Changing Network...
EpiModel-packageMathematical Modeling of Infectious Disease Dynamics
epi_trackersFunction to run the user-provided epi trackers
epiwebEpiModel Web
format_paramFormat One Parameter for Printing with the ''...
generate_random_paramsGenerate Values for Random Parameters
geom_bandsggplot2 Geom for Quantile Bands
get_argsGet Arguments from EpiModel Parameterization Functions
get_attr_historyExtract the Attributes History from Network Simulations
get_attr_propProportional Table of Vertex Attributes
get_cumulative_degreeReturn the Cumulative Degree of a Set of Index Nodes
get_cumulative_edgelistGet a Cumulative Edgelist From a Specified Network
get_cumulative_edgelists_dfGet the Cumulative Edgelists of a Model
get_current_timestepReturn the Current Timestep
get_degreeGet Individual Degree from Network or Edgelist
get_edgelistGet an Edgelist From the Specified Network
get_formula_term_attrOutput ERGM Formula Attributes into a Character Vector
get_modulesGet the List of Modules
get_networkExtract Network Objects from Network Simulations
get_network_attributesGet Network Attributes from a Network Object
get_network_term_attrOutput Network Attributes into a Character Vector
get_nwparamExtract Network Model Parameters
get_nwstatsExtract Network Statistics from netsim or netdx Object
get_param_setExtract the Parameter Set from Network Simulations
get_partnersReturn the Historical Contacts (Partners) of a Set of Index...
get_simsExtract Network Simulations
get_transmatExtract Transmissions Matrix from Network Epidemic Model
get_vertex_attributeGet Vertex Attribute on Network Object
icmStochastic Individual Contact Models
idgroupGroup Numbers for Two-Group Network
increment_timestepIncrement the Current Timestep
infection.2g.netPrimary Infection Module for netsim
infection.icmPrimary Infection Module for icm
infection.icm.bipPrimary Infection Module for icm
infection.netPrimary Infection Module for netsim
init.dcmInitial Conditions for Deterministic Compartmental Models
InitErgmTerm.absdiffbyDefinition for absdiffby ERGM Term
InitErgmTerm.absdiffnodemixDefinition for absdiffnodemix ERGM Term
InitErgmTerm.fuzzynodematchDefinition for fuzzynodematch ERGM Term
initialize.icmInitialization: icm Module
initialize.netInitialization: netsim Module
init.icmInitial Conditions for Stochastic Individual Contact Models
init.netInitial Conditions for Stochastic Network Models
init_netsNetwork Data and Stats Initialization
init_status.icmDisease Status Initialization Module for icm
init_status.netDisease Status Initialization Module for netsim
is_active_posit_idsAre These Nodes Active (Positional IDs)
is_active_unique_idsAre These Nodes Active (Unique IDs)
make_module_listPopulate the Module List After the Initialization Module is...
make_stats_tableCreate a Summary Table of Simulation Statistics
mcatWrite Out Test Progress to Console
merge.icmMerge Data across Stochastic Individual Contact Model...
merge.netsimMerge Model Simulations across netsim Objects
modules.icmModules for Stochastic Individual Contact Models
modules.netModules for Stochastic Network Models
multilayerSpecify Controls by Network
mutate_epiAdd New Epidemiology Variables
net-accessorFunctions to Access and Edit the Main netsim_dat Object in...
netdxDynamic Network Model Diagnostics
netestDynamic Network Model Estimation
netsimStochastic Network Models
netsim_cond_msgMessage to Find in Which Module a 'condition' Occurred
netsim_error_loggerHandle the Logging of Traceback and Dumping of Frames on...
network_initializeInitialize Network Object
nwupdate.netDynamic Network Updates
padded_vectorGrow a Vector to a Given Size, Padding it With Empty Elements
param.dcmEpidemic Parameters for Deterministic Compartmental Models
param.icmEpidemic Parameters for Stochastic Individual Contact Models
param.netEpidemic Parameters for Stochastic Network Models
param.net_from_tableParameters List for Stochastic Network Models from a...
param_randomCreate a Value Sampler for Random Parameters
plot.dcmPlot Data from a Deterministic Compartmental Epidemic Model
plot.icmPlot Data from a Stochastic Individual Contact Epidemic Model
plot.netdxPlot Dynamic Network Model Diagnostics
plot.netsimPlot Data from a Stochastic Network Epidemic Model
plot.transmatPlot transmat Infection Tree in Three Styles
prevalence.icmGet Epidemic Output from icm Model
prevalence.icm.bipGet Epidemic Output from icm Model
prevalence.netGet Epidemic Output from netsim Model
print.netdxUtility Function for Printing netdx Object
print_nwstats_tablePrint Helper For Network Stats Tables
process_out.netSave a List of netsim Data to Output List Format
record_attr_historyRecord Attribute History
record_raw_objectRecord an Arbitrary Object During a Simulation
recovery.2g.netRecovery: netsim Module
recovery.icmRecovery: icm Module
recovery.icm.bipRecovery: icm Module
recovery.netRecovery: netsim Module
reexportsObjects exported from other packages
remove_modulesRemove a Set of Modules From the Module List
resim_netsResimulate Dynamic Network at Time 2+
saveout.dcmSave dcm Data to Output List Format
saveout.icmSave icm Data to Output List Format
saveout.netSave netsim Data to Output List Format
set_current_timestepSet the Current Timestep
set_modulesSet the List of Modules
set_networkSet Network State During netsim Simulation
set_transmatSave Transmission Matrix
set_vertex_attributeSet Vertex Attribute on Network Object
sim_nets_t1Initialize Networks Used in netsim
simulate_datSimulate a Network for a Specified Number of Time Steps
ssampleStable Sampling Function
summary.dcmSummary Model Statistics
summary.icmSummary Model Statistics
summary.netestSummary for Network Model Fit
summary_netsExtract Summary Statistics of Networks Used in netsim
summary.netsimSummary Model Statistics
tedgelist_to_togglesConvert Timed Edgelist to Matrix of Toggles
test_icmTest the Model Output from a Stochastic Individual Contact...
test_netTest the Model Output from a Network Model
toggles_to_diss_statsConvert Matrix of Toggles to Dissolution and Duration...
trigger_end_horizonFunction to Trigger the End Horizon
trim_netestFunction to Reduce the Size of a 'netest' Object
truncate_simTruncate Simulation Time Series
unique_id-toolsConvert Unique Identifiers to/from Positional Identifiers
update_cumulative_edgelistUpdate a Cumulative Edgelist of the Specified Network
update_dissolutionAdjust Dissolution Component of Network Model Fit
update_listUpdate List 'x' Using the Elements of List 'new.x'.
update_paramsUpdate Model Parameters for Stochastic Network Models
update_unique_idsCreate the Unique Identifiers for New Nodes
use_scenarioApply a scenario object to a object
verbose.dcmProgress Print Module for Deterministic Compartmental Models
verbose.icmProgress Print Module for Stochastic Individual Contact...
verbose.netProgress Print Module for Stochastic Network Models
EpiModel documentation built on July 9, 2023, 5:21 p.m.