{
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  "Package": "DSAIDE",
  "Type": "Package",
  "Title": "Dynamical Systems Approach to Infectious Disease Epidemiology\n(Ecology/Evolution)",
  "Description": "Exploration of simulation models (apps) of various\ninfectious disease transmission dynamics scenarios. The purpose\nof the package is to help individuals learn about infectious\ndisease epidemiology (ecology/evolution) from a dynamical\nsystems perspective. All apps include explanations of the\nunderlying models and instructions on what to do with the\nmodels.",
  "Version": "0.9.6",
  "Date": "2023-08-23",
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  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "TRUE",
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  "VignetteBuilder": "knitr",
  "URL": "https://ahgroup.github.io/DSAIDE/,\nhttps://github.com/ahgroup/DSAIDE/",
  "BugReports": "https://github.com/ahgroup/DSAIDE/issues",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://ahgroup.r-universe.dev",
  "Date/Publication": "2024-01-22 17:13:43 UTC",
  "RemoteUrl": "https://github.com/ahgroup/dsaide",
  "RemoteRef": "HEAD",
  "RemoteSha": "85b543814475dedcffd17ad49cea084a72ff5892",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-23 22:20:49 UTC",
    "User": "root"
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  "Author": "Andreas Handel [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4622-1146>),\nCody Dailey [ctb],\nIsaac Chun-Hai Fung [ctb],\nRonald Galiwango [ctb],\nSalil Goyal [ctb],\nSpencer Hall [ctb],\nBen Listyg [ctb],\nBrian McKay [ctb],\nJohn Rossow [ctb],\nSina Solaimanpour [ctb],\nAlexis Vittengl [ctb],\nHenok Woldu [ctb]",
  "Maintainer": "Andreas Handel <andreas.handel@gmail.com>",
  "MD5sum": "ecdf1db77617a5a50ea82dbe0bc61565",
  "_user": "ahgroup",
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  "_created": "2026-05-23T22:20:49.000Z",
  "_published": "2026-05-23T22:24:56.731Z",
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    "extra/readme.md",
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    },
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    "dsaidemenu",
    "generate_documentation",
    "generate_fctcall",
    "generate_ggplot",
    "generate_plotly",
    "generate_shinyinput",
    "generate_text",
    "run_model",
    "simulate_Characteristics_of_ID_ode",
    "simulate_Complex_ID_Control_ode",
    "simulate_directtransmission_ode",
    "simulate_Drug_Resistance_Evolution_stochastic",
    "simulate_Environmental_Transmission_model_ode",
    "simulate_flu_fit",
    "simulate_Host_Heterogeneity_Model_ode",
    "simulate_idcontrolmultigroup_ode",
    "simulate_idcontrolmultioutbreak_ode",
    "simulate_idpatterns_ode",
    "simulate_idsurveillance_ode",
    "simulate_idvaccine_ode",
    "simulate_multipathogen_ode",
    "simulate_noro_fit",
    "simulate_SEIRSd_model_stochastic",
    "simulate_SIR_model_discrete",
    "simulate_SIR_model_ode",
    "simulate_SIR_modelexploration",
    "simulate_SIR_usanalysis",
    "simulate_SIRSd_model_ode",
    "simulate_SIRSd_model_stochastic",
    "simulate_Vector_transmission_model_ode"
  ],
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      "title": "1918 Influenza mortality data",
      "object": "flu1918data",
      "class": [
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        "tbl",
        "data.frame"
      ],
      "fields": [
        "Date",
        "Deaths"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    },
    {
      "name": "norodata",
      "title": "Cases of norovirus during an outbreak",
      "object": "norodata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Date",
        "Cases"
      ],
      "rows": 10,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "dsaidemenu",
      "title": "The main menu for the DSAIDE package",
      "topics": [
        "dsaidemenu"
      ]
    },
    {
      "page": "flu1918data",
      "title": "1918 Influenza mortality data",
      "topics": [
        "flu1918data"
      ]
    },
    {
      "page": "generate_documentation",
      "title": "A helper function which processes and displays the documentation part for each app",
      "topics": [
        "generate_documentation"
      ]
    },
    {
      "page": "generate_fctcall",
      "title": "A helper function that produces a call to a simulator function for specific settings",
      "topics": [
        "generate_fctcall"
      ]
    },
    {
      "page": "generate_ggplot",
      "title": "A helper function that takes simulation results and produces ggplot plots",
      "topics": [
        "generate_ggplot"
      ]
    },
    {
      "page": "generate_plotly",
      "title": "A helper function that takes simulation results and produces plotly plots",
      "topics": [
        "generate_plotly"
      ]
    },
    {
      "page": "generate_shinyinput",
      "title": "A helper function that takes a model and generates shiny UI elements",
      "topics": [
        "generate_shinyinput"
      ]
    },
    {
      "page": "generate_text",
      "title": "A helper function that takes result from the simulators and produces text output",
      "topics": [
        "generate_text"
      ]
    },
    {
      "page": "norodata",
      "title": "Cases of norovirus during an outbreak",
      "topics": [
        "norodata"
      ]
    },
    {
      "page": "run_model",
      "title": "A function that runs an app for specific settings and processes results for plot and text generation",
      "topics": [
        "run_model"
      ]
    },
    {
      "page": "simulate_Characteristics_of_ID_ode",
      "title": "Characteristics of ID",
      "topics": [
        "simulate_Characteristics_of_ID_ode"
      ]
    },
    {
      "page": "simulate_Complex_ID_Control_ode",
      "title": "Complex ID Control",
      "topics": [
        "simulate_Complex_ID_Control_ode"
      ]
    },
    {
      "page": "simulate_directtransmission_ode",
      "title": "Simulation of a compartmental infectious disease transmission model illustrating different types of direct transmission",
      "topics": [
        "simulate_directtransmission_ode"
      ]
    },
    {
      "page": "simulate_Drug_Resistance_Evolution_stochastic",
      "title": "Drug Resistance Evolution",
      "topics": [
        "simulate_Drug_Resistance_Evolution_stochastic"
      ]
    },
    {
      "page": "simulate_Environmental_Transmission_model_ode",
      "title": "Environmental Transmission model",
      "topics": [
        "simulate_Environmental_Transmission_model_ode"
      ]
    },
    {
      "page": "simulate_flu_fit",
      "title": "Fitting a SIR-type model to flu data",
      "topics": [
        "simulate_flu_fit"
      ]
    },
    {
      "page": "simulate_Host_Heterogeneity_Model_ode",
      "title": "Host Heterogeneity Model",
      "topics": [
        "simulate_Host_Heterogeneity_Model_ode"
      ]
    },
    {
      "page": "simulate_idcontrolmultigroup_ode",
      "title": "Simulation of a compartmental infectious disease transmission model with 3 types of hosts and intervention",
      "topics": [
        "simulate_idcontrolmultigroup_ode"
      ]
    },
    {
      "page": "simulate_idcontrolmultioutbreak_ode",
      "title": "Simulation of a compartmental infectious disease transmission model to study the reproductive number",
      "topics": [
        "simulate_idcontrolmultioutbreak_ode"
      ]
    },
    {
      "page": "simulate_idpatterns_ode",
      "title": "Simulation of a compartmental infectious disease transmission model including seasonality",
      "topics": [
        "simulate_idpatterns_ode"
      ]
    },
    {
      "page": "simulate_idsurveillance_ode",
      "title": "Simulation of a compartmental infectious disease transmission model illustrating the impact of ID surveillance",
      "topics": [
        "simulate_idsurveillance_ode"
      ]
    },
    {
      "page": "simulate_idvaccine_ode",
      "title": "Simulation of a compartmental infectious disease transmission model to study the reproductive number",
      "topics": [
        "simulate_idvaccine_ode"
      ]
    },
    {
      "page": "simulate_multipathogen_ode",
      "title": "Simulation of a compartmental infectious disease transmission model with 2 types of pathogens",
      "topics": [
        "simulate_multipathogen_ode"
      ]
    },
    {
      "page": "simulate_noro_fit",
      "title": "Fitting a simple SIR type model to norovirus outbreak data",
      "topics": [
        "simulate_noro_fit"
      ]
    },
    {
      "page": "simulate_SEIRSd_model_stochastic",
      "title": "SEIRSd model",
      "topics": [
        "simulate_SEIRSd_model_stochastic"
      ]
    },
    {
      "page": "simulate_SIR_model_discrete",
      "title": "SIR model",
      "topics": [
        "simulate_SIR_model_discrete"
      ]
    },
    {
      "page": "simulate_SIR_model_ode",
      "title": "SIR model",
      "topics": [
        "simulate_SIR_model_ode"
      ]
    },
    {
      "page": "simulate_SIR_modelexploration",
      "title": "Simulation to illustrate parameter scan of the basic SIR model with births and deaths #'",
      "topics": [
        "simulate_SIR_modelexploration"
      ]
    },
    {
      "page": "simulate_SIR_usanalysis",
      "title": "Simulation to illustrate uncertainty and sensitivity analysis",
      "topics": [
        "simulate_SIR_usanalysis"
      ]
    },
    {
      "page": "simulate_SIRSd_model_ode",
      "title": "SIRSd model",
      "topics": [
        "simulate_SIRSd_model_ode"
      ]
    },
    {
      "page": "simulate_SIRSd_model_stochastic",
      "title": "SIRSd model",
      "topics": [
        "simulate_SIRSd_model_stochastic"
      ]
    },
    {
      "page": "simulate_Vector_transmission_model_ode",
      "title": "Vector transmission model",
      "topics": [
        "simulate_Vector_transmission_model_ode"
      ]
    }
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      "title": "DSAIDE Package Tutorial",
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      "engine": "knitr::rmarkdown",
      "headings": [
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        "Package description",
        "Intended audience and goal of the package",
        "Pre-requisites",
        "Installation",
        "Using the package",
        "Level 1: Interactive use through the graphical user interface",
        "Load and run the package",
        "Level 2: Directly interacting with the simulation functions",
        "Level 3: Modifying the simulation functions",
        "Contributing to the package",
        "Further information",
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        "Citation",
        "References"
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      "created": "2016-08-11 19:37:52",
      "modified": "2023-08-22 11:38:19",
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