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  "Date": "2026-05-18",
  "Title": "Mathematical Modeling of Infectious Disease Dynamics",
  "Description": "Tools for simulating mathematical models of infectious\ndisease dynamics. Epidemic model classes include deterministic\ncompartmental models, stochastic individual-contact models, and\nstochastic network models. Network models use the robust\nstatistical methods of exponential-family random graph models\n(ERGMs) from the Statnet suite of software packages in R.\nStandard templates for epidemic modeling include SI, SIR, and\nSIS disease types. EpiModel features an API for extending these\ntemplates to address novel scientific research aims. Full\nmethods for EpiModel are detailed in Jenness et al. (2018,\n<doi:10.18637/jss.v084.i08>).",
  "Maintainer": "Samuel Jenness <samuel.m.jenness@emory.edu>",
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  "Date/Publication": "2026-05-30 21:41:20 UTC",
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    "message": "Fix1045 (#1046)\n\n* fix `create_scenario_list`\n\nfix 1045\n\n* Fix generate_random_params on single-column param.random.set\n\nSame root cause as create_scenario_list: indexing a one-column\ndata.frame row drops it to an unnamed vector, so unflatten_params\nsees NULL names and errors on strsplit. Use drop = FALSE here too.\n\n---------\n\nCo-authored-by: Samuel Jenness <smjenness@gmail.com>",
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    "get_param",
    "get_param_list",
    "get_param_set",
    "get_partners",
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    "infection.icm",
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    "verbose.dcm",
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    "verbose.net"
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  "_help": [
    {
      "page": "EpiModel-package",
      "title": "Mathematical Modeling of Infectious Disease Dynamics",
      "topics": [
        "EpiModel-package",
        "EpiModel"
      ]
    },
    {
      "page": "add_vertices",
      "title": "Fast Version of network::add.vertices for Edgelist-formatted Network",
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    },
    {
      "page": "apportion_lr",
      "title": "Apportion Using the Largest Remainder Method",
      "topics": [
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    {
      "page": "arrive_nodes",
      "title": "Arrive New Nodes to the netsim_dat Object",
      "topics": [
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    {
      "page": "as_cumulative_edgelist",
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      "topics": [
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    },
    {
      "page": "as_tibble_edgelist",
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      "topics": [
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      ]
    },
    {
      "page": "as.data.frame.dcm",
      "title": "Extract Model Data for Deterministic Compartmental Models",
      "topics": [
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    },
    {
      "page": "as.data.frame.icm",
      "title": "Extract Model Data for Stochastic Models",
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    {
      "page": "as.data.frame.netdx",
      "title": "Extract Timed Edgelists for netdx Objects",
      "topics": [
        "as.data.frame.netdx"
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    {
      "page": "as.epi.data.frame",
      "title": "Validate and Convert to epi.data.frame",
      "topics": [
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    },
    {
      "page": "as.network.transmat",
      "title": "Convert transmat Infection Tree into a network Object",
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    {
      "page": "as.phylo.transmat",
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    {
      "page": "check_degdist_bal",
      "title": "Check Degree Distribution for Balance in Target Statistics",
      "topics": [
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    },
    {
      "page": "color_tea",
      "title": "Create a TEA Variable for Infection Status for 'ndtv' Animations",
      "topics": [
        "color_tea"
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    },
    {
      "page": "comp_plot",
      "title": "Plot Compartment Diagram for Epidemic Models",
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        "comp_plot.dcm",
        "comp_plot.icm",
        "comp_plot.netsim"
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    {
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    {
      "page": "control.icm",
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      "page": "control.net",
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      "page": "dedup_cumulative_edgelist",
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      "topics": [
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    },
    {
      "page": "delete_edges",
      "title": "Remove Edges That Include Specified Vertices",
      "topics": [
        "delete_edges"
      ]
    },
    {
      "page": "delete_vertices",
      "title": "Fast Version of network::delete.vertices for Edgelist-formatted Network",
      "topics": [
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    },
    {
      "page": "depart_nodes",
      "title": "Depart Nodes from the netsim_dat Object",
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        "depart_nodes"
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    },
    {
      "page": "dissolution_coefs",
      "title": "Dissolution Coefficients for Stochastic Network Models",
      "topics": [
        "dissolution_coefs"
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    },
    {
      "page": "edgelist_censor",
      "title": "Table of Edge Censoring",
      "topics": [
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    },
    {
      "page": "epiweb",
      "title": "EpiModel Web",
      "topics": [
        "epiweb"
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    {
      "page": "generate_random_params",
      "title": "Generate Values for Random Parameters",
      "topics": [
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    },
    {
      "page": "geom_bands",
      "title": "ggplot2 Geom for Quantile Bands",
      "topics": [
        "geom_bands"
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    },
    {
      "page": "get_adj_list",
      "title": "Returns an adjacency list from an edge list",
      "topics": [
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    },
    {
      "page": "get_attr_history",
      "title": "Extract the Attributes History from Network Simulations",
      "topics": [
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    },
    {
      "page": "get_connected_nodes",
      "title": "Returns all the node connected directly or indirectly to a set of nodes",
      "topics": [
        "get_connected_nodes"
      ]
    },
    {
      "page": "get_cumulative_degree",
      "title": "Return the Cumulative Degree of a Set of Index Nodes",
      "concept": [
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      ],
      "topics": [
        "get_cumulative_degree"
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    },
    {
      "page": "get_cumulative_edgelist",
      "title": "Get a Cumulative Edgelist From a Specified Network",
      "concept": [
        "cumulative_edgelist"
      ],
      "topics": [
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    },
    {
      "page": "get_cumulative_edgelists_df",
      "title": "Get the Cumulative Edgelists of a Model",
      "concept": [
        "cumulative_edgelist"
      ],
      "topics": [
        "get_cumulative_edgelists_df"
      ]
    },
    {
      "page": "get_current_timestep",
      "title": "Return the Current Timestep",
      "topics": [
        "get_current_timestep"
      ]
    },
    {
      "page": "get_degree",
      "title": "Get Individual Degree from Network or Edgelist",
      "topics": [
        "get_degree"
      ]
    },
    {
      "page": "get_edgelist",
      "title": "Get an Edgelist From the Specified Network",
      "topics": [
        "get_edgelist"
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    },
    {
      "page": "get_edgelists_df",
      "title": "Get the Edgelist(s) from the Specified Network(s)",
      "topics": [
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    },
    {
      "page": "get_formula_term_attr",
      "title": "Output ERGM Formula Attributes into a Character Vector",
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    {
      "page": "get_network",
      "title": "Extract Network Objects from Network Simulations",
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        "get_network.netdx",
        "get_network.netsim",
        "get_network.netsim_dat"
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    },
    {
      "page": "get_network_attributes",
      "title": "Get Network Attributes from a Network Object",
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    {
      "page": "get_network_term_attr",
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    {
      "page": "get_nwstats",
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      "topics": [
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    },
    {
      "page": "get_param_set",
      "title": "Extract the Parameter Set from Network Simulations",
      "topics": [
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    },
    {
      "page": "get_partners",
      "title": "Return the Historical Contacts (Partners) of a Set of Index Nodes",
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      "topics": [
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    {
      "page": "get_sims",
      "title": "Extract Network Simulations",
      "topics": [
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    },
    {
      "page": "get_subnet_adj_list",
      "title": "Return an adjacency list of subnets",
      "topics": [
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    },
    {
      "page": "get_vertex_attribute",
      "title": "Get Vertex Attribute on Network Object",
      "topics": [
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    },
    {
      "page": "icm",
      "title": "Stochastic Individual Contact Models",
      "topics": [
        "icm"
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    },
    {
      "page": "increment_timestep",
      "title": "Increment the Current Timestep",
      "topics": [
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    },
    {
      "page": "init.dcm",
      "title": "Initial Conditions for Deterministic Compartmental Models",
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    {
      "page": "init.icm",
      "title": "Initial Conditions for Stochastic Individual Contact Models",
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    },
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      "page": "init.net",
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    {
      "page": "InitErgmTerm.absdiffby",
      "title": "Definition for absdiffby ERGM Term",
      "topics": [
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        "InitErgmTerm.absdiffby"
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    },
    {
      "page": "InitErgmTerm.absdiffnodemix",
      "title": "Definition for absdiffnodemix ERGM Term",
      "topics": [
        "absdiffnodemix",
        "InitErgmTerm.absdiffnodemix"
      ]
    },
    {
      "page": "InitErgmTerm.fuzzynodematch",
      "title": "Definition for fuzzynodematch ERGM Term",
      "topics": [
        "fuzzynodematch",
        "InitErgmTerm.fuzzynodematch"
      ]
    },
    {
      "page": "is_active_posit_ids",
      "title": "Are These Nodes Active (Positional IDs)",
      "topics": [
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    },
    {
      "page": "is_active_unique_ids",
      "title": "Are These Nodes Active (Unique IDs)",
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    },
    {
      "page": "get_transmat",
      "title": "Extract Transmissions Matrix from Network Epidemic Model",
      "topics": [
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        "is.transmat",
        "transmat"
      ]
    },
    {
      "page": "make_restart_point",
      "title": "Make a Lightweight Restart Point From a 'netsim' Object with tergmLite",
      "topics": [
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      ]
    },
    {
      "page": "merge.icm",
      "title": "Merge Data across Stochastic Individual Contact Model Simulations",
      "topics": [
        "merge.icm"
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    },
    {
      "page": "merge.netsim",
      "title": "Merge Model Simulations across netsim Objects",
      "topics": [
        "merge.netsim"
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    },
    {
      "page": "modules.icm",
      "title": "Modules for Stochastic Individual Contact Models",
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    },
    {
      "page": "modules.net",
      "title": "Modules for Stochastic Network Models",
      "topics": [
        "modules.net"
      ]
    },
    {
      "page": "multilayer",
      "title": "Specify Controls by Network",
      "topics": [
        "multilayer"
      ]
    },
    {
      "page": "mutate_epi",
      "title": "Add New Epidemiology Variables",
      "topics": [
        "mutate_epi"
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    },
    {
      "page": "net-accessor",
      "title": "Functions to Access and Edit the Main netsim_dat Object in Network Models",
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        "add_control",
        "add_epi",
        "add_init",
        "add_param",
        "append_attr",
        "append_core_attr",
        "get_attr",
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        "get_control",
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        "set_control",
        "set_epi",
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        "set_param"
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    },
    {
      "page": "netdx",
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    {
      "page": "netest",
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      "topics": [
        "netest"
      ]
    },
    {
      "page": "netsim",
      "title": "Stochastic Network Models",
      "topics": [
        "netsim"
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    },
    {
      "page": "network_initialize",
      "title": "Initialize Network Object",
      "topics": [
        "network_initialize"
      ]
    },
    {
      "page": "nwupdate.net",
      "title": "Dynamic Network Updates",
      "topics": [
        "nwupdate.net"
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    },
    {
      "page": "overwrite_attrs",
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      "topics": [
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    },
    {
      "page": "padded_vector",
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      "topics": [
        "padded_vector"
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    },
    {
      "page": "param_random",
      "title": "Create a Value Sampler for Random Parameters",
      "topics": [
        "param_random"
      ]
    },
    {
      "page": "param.dcm",
      "title": "Epidemic Parameters for Deterministic Compartmental Models",
      "topics": [
        "param.dcm"
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    },
    {
      "page": "param.icm",
      "title": "Epidemic Parameters for Stochastic Individual Contact Models",
      "topics": [
        "param.icm"
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    },
    {
      "page": "param.net",
      "title": "Epidemic Parameters for Stochastic Network Models",
      "topics": [
        "param.net"
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    },
    {
      "page": "param.net_from_table",
      "title": "Parameters List for Stochastic Network Models from a Formatted Data Frame",
      "topics": [
        "param.net_from_table"
      ]
    },
    {
      "page": "param.net_to_table",
      "title": "Coerce a list of parameters to a 'long.param.df'",
      "topics": [
        "param.net_to_table"
      ]
    },
    {
      "page": "plot.dcm",
      "title": "Plot Data from a Deterministic Compartmental Epidemic Model",
      "topics": [
        "plot.dcm"
      ]
    },
    {
      "page": "plot.epi.data.frame",
      "title": "Plot Epidemic Model Results From a Netsim Data.Frame",
      "topics": [
        "plot.epi.data.frame"
      ]
    },
    {
      "page": "plot.icm",
      "title": "Plot Data from a Stochastic Individual Contact Epidemic Model",
      "topics": [
        "plot.icm"
      ]
    },
    {
      "page": "plot.netdx",
      "title": "Plot Dynamic Network Model Diagnostics",
      "topics": [
        "plot.netdx"
      ]
    },
    {
      "page": "plot.netsim",
      "title": "Plot Data from a Stochastic Network Epidemic Model",
      "topics": [
        "plot.netsim"
      ]
    },
    {
      "page": "plot.transmat",
      "title": "Plot transmat Infection Tree in Three Styles",
      "topics": [
        "plot.transmat"
      ]
    },
    {
      "page": "print.dcm",
      "title": "Print Method for DCM Objects",
      "topics": [
        "print.dcm"
      ]
    },
    {
      "page": "print.icm",
      "title": "Print Method for ICM Objects",
      "topics": [
        "print.icm"
      ]
    },
    {
      "page": "print.netdx",
      "title": "Utility Function for Printing netdx Object",
      "topics": [
        "print.netdx"
      ]
    },
    {
      "page": "print.netsim",
      "title": "Print Method for Network Model Simulations",
      "topics": [
        "print.netsim"
      ]
    },
    {
      "page": "reachable-nodes",
      "title": "Get the Forward or Backward Reachable Nodes for a Set of Nodes",
      "concept": [
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        "get_forward_reachable",
        "reachable-nodes"
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    {
      "page": "record_attr_history",
      "title": "Record Attribute History",
      "topics": [
        "record_attr_history"
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    },
    {
      "page": "record_raw_object",
      "title": "Record an Arbitrary Object During a Simulation",
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    },
    {
      "page": "set_current_timestep",
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        "set_current_timestep"
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    {
      "page": "set_transmat",
      "title": "Save Transmission Matrix",
      "topics": [
        "set_transmat"
      ]
    },
    {
      "page": "set_vertex_attribute",
      "title": "Set Vertex Attribute on Network Object",
      "topics": [
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    },
    {
      "page": "summary.dcm",
      "title": "Summary Model Statistics",
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    },
    {
      "page": "summary.icm",
      "title": "Summary Model Statistics",
      "topics": [
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      ]
    },
    {
      "page": "summary.netsim",
      "title": "Summary Model Statistics",
      "topics": [
        "summary.netsim"
      ]
    },
    {
      "page": "trim_netest",
      "title": "Function to Reduce the Size of a 'netest' Object",
      "topics": [
        "trim_netest"
      ]
    },
    {
      "page": "truncate_sim",
      "title": "Truncate Simulation Time Series",
      "topics": [
        "truncate_sim",
        "truncate_sim.dcm",
        "truncate_sim.icm",
        "truncate_sim.netsim"
      ]
    },
    {
      "page": "unique_id-tools",
      "title": "Convert Unique Identifiers to/from Positional Identifiers",
      "topics": [
        "get_posit_ids",
        "get_unique_ids",
        "unique_id-tools"
      ]
    },
    {
      "page": "update_cumulative_edgelist",
      "title": "Update a Cumulative Edgelist of the Specified Network",
      "concept": [
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      "topics": [
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    },
    {
      "page": "update_dissolution",
      "title": "Adjust Dissolution Component of Network Model Fit",
      "topics": [
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      ]
    },
    {
      "page": "update_params",
      "title": "Update Model Parameters for Stochastic Network Models",
      "topics": [
        "update_params"
      ]
    },
    {
      "page": "use_scenario",
      "title": "Apply a scenario object to a param.net object",
      "topics": [
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