Man pages for EpiModel
Mathematical Modeling of Infectious Disease Dynamics
| add_vertices | Fast Version of network::add.vertices for Edgelist-formatted... |
| apportion_lr | Apportion Using the Largest Remainder Method |
| arrivals.2g.net | Arrivals: netsim Module |
| arrivals.icm | Arrivals: icm Module |
| arrivals.icm.bip | Arrivals: Bipartite icm Module |
| arrivals.net | Arrivals: netsim Module |
| arrive_nodes | Arrive New Nodes to the netsim_dat Object |
| as_cumulative_edgelist | Convert an object to a 'cumulative_edgelist' |
| 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.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_tibble_edgelist | Convert an Edgelist into a Tibble |
| auto_update_attr | Update Vertex Attributes for Incoming Vertices |
| brewer_ramp | RColorBrewer Color Ramp for EpiModel Plots |
| check_attr_lengths | Check that All Attributes in the Main 'netsim_dat' Object are... |
| check_degdist_bal | Check Degree Distribution for Balance in Target Statistics |
| check_end_horizon_control | Check the format of the end.horizon control |
| color_tea | Create a TEA Variable for Infection Status for 'ndtv'... |
| common_updater | Update Either the "param" or "control" List |
| 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 |
| copy_datattr_to_nwattr | Copy Vertex Attributes from the 'netsim_dat' List to the... |
| copy_nwattr_to_datattr | Copy Vertex Attributes From Network to 'netsim_dat' List |
| create_dat_object | Create a Minimal netsim_dat Main List Object for a Network... |
| create_scenario_list | Make a list of EpiModel scenarios from a data.frame of... |
| crosscheck.dcm | Cross Checking of Inputs for Deterministic Compartmental... |
| crosscheck.icm | Cross Checking of Inputs for Stochastic Individual Contact... |
| crosscheck.net | Cross Checking of Inputs for Stochastic Network Models |
| dcm | Deterministic Compartmental Models |
| dcm.mods | Deterministic Compartmental Model Functions |
| dedup_cumulative_edgelist | Deduplicate a cumulative edgelist by combining overlapping... |
| delete_attr | Delete Elements from Attribute List |
| delete_edges | Remove Edges That Include Specified Vertices |
| delete_vertices | Fast Version of network::delete.vertices for... |
| depart_nodes | Depart Nodes from the netsim_dat Object |
| departures.2g.net | Departures: netsim Module |
| departures.icm | Departure: icm Module |
| departures.icm.bip | Departure: Bipartite icm Module |
| departures.net | Departures: netsim Module |
| discord_edgelist | Discordant Edgelist |
| dissolution_coefs | Dissolution Coefficients for Stochastic Network Models |
| edgelist_censor | Table of Edge Censoring |
| edges_correct | Adjustment for the Edges Coefficient with Changing Network... |
| EpiModel-package | Mathematical Modeling of Infectious Disease Dynamics |
| epi_trackers | Function to run the user-provided epi trackers |
| epiweb | EpiModel Web |
| format_param | Format One Parameter for Printing with the 'print.param.xxx'... |
| 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_args | Get Arguments from EpiModel Parameterization Functions |
| get_attr_history | Extract the Attributes History from Network Simulations |
| get_attr_prop | Proportional Table of Vertex Attributes |
| get_connected_nodes | Returns all the node connected directly or indirectly to a... |
| 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_discordant_edgelist | Get Discordant Edgelist Based on Specified Status Variable |
| 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_modules | Get the List of Modules |
| 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_nwparam | Extract Network Model Parameters |
| 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... |
| 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_vertex_attribute | Get Vertex Attribute on Network Object |
| icm | Stochastic Individual Contact Models |
| idgroup | Group Numbers for Two-Group Network |
| increment_timestep | Increment the Current Timestep |
| infection.2g.net | Primary Infection Module for netsim |
| infection.icm | Primary Infection Module for icm |
| infection.icm.bip | Primary Infection Module for icm |
| infection.net | Primary Infection Module for netsim |
| init.dcm | Initial Conditions for Deterministic Compartmental Models |
| InitErgmTerm.absdiffby | Definition for absdiffby ERGM Term |
| InitErgmTerm.absdiffnodemix | Definition for absdiffnodemix ERGM Term |
| InitErgmTerm.fuzzynodematch | Definition for fuzzynodematch ERGM Term |
| initialize.icm | Initialization: icm Module |
| initialize.net | Initialization: netsim Module |
| init.icm | Initial Conditions for Stochastic Individual Contact Models |
| init.net | Initial Conditions for Stochastic Network Models |
| init_nets | Network Data and Stats Initialization |
| init_status.icm | Disease Status Initialization Module for icm |
| init_status.net | Disease Status Initialization Module for netsim |
| is_active_posit_ids | Are These Nodes Active (Positional IDs) |
| is_active_unique_ids | Are These Nodes Active (Unique IDs) |
| make_module_list | Populate the Module List After the Initialization Module is... |
| make_stats_table | Create a Summary Table of Simulation Statistics |
| mcat | Write Out Test Progress to Console |
| merge.icm | Merge Data across Stochastic Individual Contact Model... |
| 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 |
| net-accessor | Functions to Access and Edit the Main netsim_dat Object in... |
| netdx | Dynamic Network Model Diagnostics |
| netest | Dynamic Network Model Estimation |
| netsim | Stochastic Network Models |
| netsim_cond_msg | Message to Find in Which Module a 'condition' Occurred |
| netsim_error_logger | Handle the Logging of Traceback and Dumping of Frames on... |
| 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... |
| 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 |
| prevalence.icm | Get Epidemic Output from icm Model |
| prevalence.icm.bip | Get Epidemic Output from icm Model |
| prevalence.net | Get Epidemic Output from netsim Model |
| print.netdx | Utility Function for Printing netdx Object |
| print_nwstats_table | Print Helper For Network Stats Tables |
| process_out.net | Save a List of netsim Data to Output List Format |
| reachable-nodes | Get the Forward or Backward Reachable Nodes for a Set of... |
| record_attr_history | Record Attribute History |
| record_raw_object | Record an Arbitrary Object During a Simulation |
| recovery.2g.net | Recovery: netsim Module |
| recovery.icm | Recovery: icm Module |
| recovery.icm.bip | Recovery: icm Module |
| recovery.net | Recovery: netsim Module |
| remove_modules | Remove a Set of Modules From the Module List |
| resim_nets | Resimulate Dynamic Network at Time 2+ |
| saveout.dcm | Save dcm Data to Output List Format |
| saveout.icm | Save icm Data to Output List Format |
| saveout.net | Save netsim Data to Output List Format |
| set_current_timestep | Set the Current Timestep |
| set_modules | Set the List of Modules |
| set_network | Set Network State During netsim Simulation |
| set_transmat | Save Transmission Matrix |
| set_vertex_attribute | Set Vertex Attribute on Network Object |
| sim_nets_t1 | Initialize Networks Used in netsim |
| simulate_dat | Simulate a Network for a Specified Number of Time Steps |
| ssample | Stable Sampling Function |
| summary.dcm | Summary Model Statistics |
| summary.icm | Summary Model Statistics |
| summary.netest | Summary for Network Model Fit |
| summary_nets | Extract Summary Statistics of Networks Used in netsim |
| summary.netsim | Summary Model Statistics |
| tedgelist_to_toggles | Convert Timed Edgelist to Matrix of Toggles |
| test_icm | Test the Model Output from a Stochastic Individual Contact... |
| test_net | Test the Model Output from a Network Model |
| toggles_to_diss_stats | Convert Matrix of Toggles to Dissolution and Duration... |
| trigger_end_horizon | Function to Trigger the End Horizon |
| trim_netest | Function to Reduce the Size of a 'netest' Object |
| truncate_sim | Truncate Simulation Time Series |
| 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_list | Update List 'x' Using the Elements of List 'new.x'. |
| update_params | Update Model Parameters for Stochastic Network Models |
| update_unique_ids | Create the Unique Identifiers for New Nodes |
| use_scenario | Apply a scenario object to a param.net object |
| verbose.dcm | Progress Print Module for Deterministic Compartmental Models |
| verbose.icm | Progress Print Module for Stochastic Individual Contact... |
| verbose.net | Progress Print Module for Stochastic Network Models |
