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  "Version": "1.0.3",
  "Date": "2023-04-28",
  "Title": "Explicit Interaction Community Models",
  "Authors@R": "c(person(given=\"Miguel\", family=\"Porto\",\nemail=\"mpbertolo@gmail.com\", comment = c(ORCID=\"0000-0001-7640-0623\"), role=c(\"aut\", \"cre\")),\nperson(given=\"Pedro\", family=\"Beja\", comment = c(ORCID=\"0000-0001-8164-0760\"), role=\"aut\"))",
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  "VignetteBuilder": "knitr",
  "Description": "Model fitting and species biotic interaction network\ntopology selection for explicit interaction community models.\nExplicit interaction community models are an extension of\nbinomial linear models for joint modelling of species\ncommunities, that incorporate both the effects of species\nbiotic interactions and the effects of missing covariates.\nSpecies interactions are modelled as direct effects of each\nspecies on each of the others, and are estimated alongside the\neffects of missing covariates, modelled as latent factors. The\npackage includes a penalized maximum likelihood fitting\nfunction, and a genetic algorithm for selecting the most\nparsimonious species interaction network topology.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "URL": "https://github.com/miguel-porto/eicm",
  "BugReports": "https://github.com/miguel-porto/eicm",
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  "Repository": "https://miguel-porto.r-universe.dev",
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  "Author": "Miguel Porto [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7640-0623>),\nPedro Beja [aut] (ORCID: <https://orcid.org/0000-0001-8164-0760>)",
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    "ecological-modelling",
    "interaction-network",
    "joint-models",
    "jsdm",
    "missing-covariates",
    "species-distribution-modelling",
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    "eicm.data",
    "eicm.fit",
    "eicm.matrix",
    "eicm.options",
    "generateEICM",
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      "title": "A parameterized EICM model for simulation",
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      "title": "eicm: Explicit Interaction Community Models",
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    {
      "page": "as.eicm",
      "title": "Define a parameterized EICM model",
      "topics": [
        "as.eicm"
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    },
    {
      "page": "coef.eicm",
      "title": "Extract EICM model coefficients",
      "topics": [
        "coef.eicm"
      ]
    },
    {
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      "title": "Diagnostic monitor plots for EICM",
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      ]
    },
    {
      "page": "confint.eicm",
      "title": "Confidence intervals for EICM parameters",
      "topics": [
        "confint.eicm"
      ]
    },
    {
      "page": "eicm",
      "title": "Fit and select an Explicit Interaction Community Model (EICM)",
      "topics": [
        "eicm"
      ]
    },
    {
      "page": "eicm.data",
      "title": "Define a data object for a EICM model",
      "topics": [
        "eicm.data"
      ]
    },
    {
      "page": "eicm.fit",
      "title": "Estimate a EICM model",
      "topics": [
        "eicm.fit"
      ]
    },
    {
      "page": "eicm.matrix",
      "title": "Define a model object for a EICM model",
      "topics": [
        "eicm.matrix"
      ]
    },
    {
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      "title": "Set EICM fitting options",
      "topics": [
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      ]
    },
    {
      "page": "generateEICM",
      "title": "Generate EICM model following a Beta frequency distribution",
      "topics": [
        "generateEICM"
      ]
    },
    {
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      "title": "Compare two interaction matrices",
      "topics": [
        "interactionPlot"
      ]
    },
    {
      "page": "isCyclic",
      "title": "Is the adjacency matrix a cyclic graph?",
      "topics": [
        "isCyclic"
      ]
    },
    {
      "page": "logLik.eicm",
      "title": "EICM (penalized) log-likelihood",
      "topics": [
        "logLik.eicm"
      ]
    },
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      "title": "Plot EICM estimates and confidence intervals",
      "topics": [
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      "title": "Quick plot EICM results",
      "topics": [
        "plot.eicm"
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    },
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      "title": "Quick plot EICM results",
      "topics": [
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      "title": "Print EICM model matrix",
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      "title": "A parameterized EICM model for simulation",
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      "title": "Explicit Interaction Community Models",
      "author": "Miguel Porto, Pedro Beja^[CIBIO/InBio – Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal]",
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        "Formula syntax",
        "Matrix syntax",
        "Fitting without selecting network",
        "Fitting with NAs in the response",
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        "Simulating species communities",
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      "created": "2020-03-27 15:06:11",
      "modified": "2020-03-27 15:06:11",
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