{
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  "Package": "CooccurrenceAffinity",
  "Type": "Package",
  "Title": "Affinity in Co-Occurrence Data",
  "Version": "2.0.0",
  "Date": "2026-01-27",
  "Authors@R": "c(\nperson(\"Kumar\", \"Mainali\", role = c(\"aut\", \"cre\"), email = \"kpmainali@gmail.com\"),\nperson(\"Eric\", \"Slud\", role = c(\"aut\"))\n)",
  "Description": "Computes a novel metric of affinity between two entities\nbased on their co-occurrence (using binary presence/absence\ndata). The metric and its maximum likelihood estimator (alpha\nhat) were advanced in Mainali, Slud, et al, 2021\n<doi:10.1126/sciadv.abj9204>. Four types of confidence\nintervals and median interval were developed in Mainali and\nSlud, 2022 <doi:10.1101/2022.11.01.514801>. The `finches`\ndataset is bundled with the package.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
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  "BugReports": "https://github.com/kpmainali/CooccurrenceAffinity/issues",
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  "Date/Publication": "2026-01-28 23:51:40 UTC",
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  "Maintainer": "Kumar Mainali <kpmainali@gmail.com>",
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      "date": "2025-06-27"
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      "date": "2026-02-16"
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    "AcceptAffin",
    "affinity",
    "affinity2by2",
    "AlphInts",
    "Bisect",
    "Covrg",
    "CovrgPlot",
    "dataprep",
    "EHypMidP",
    "EHypQuInt",
    "logLikExtHyp",
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    "midP.EHyp",
    "minmaxAlpha.pFNCH",
    "MinX.Int",
    "ML.Alpha",
    "plotgg"
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      "title": "Darwin’s finches presence–absence data",
      "object": "finches",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Seymour",
        "Baltra",
        "Isabella",
        "Fernandina",
        "Santiago",
        "Rabida",
        "Pinzon",
        "Santa.Cruz",
        "Santa.Fe",
        "San.Cristobal",
        "Espanola",
        "Floreana",
        "Genovesa",
        "Marchena",
        "Pinta",
        "Darwin",
        "Wolf"
      ],
      "rows": 13,
      "table": true,
      "tojson": true
    }
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    {
      "page": "AcceptAffCI",
      "title": "Acceptability Interval",
      "topics": [
        "AcceptAffCI"
      ]
    },
    {
      "page": "AcceptAffin",
      "title": "Calculates the \"Acceptability Function\" used in defining Blaker's (2000) Acceptability Interval and computing the latter in the function AcceptAffCI().",
      "topics": [
        "AcceptAffin"
      ]
    },
    {
      "page": "affinity",
      "title": "Computes alpha, probability, expected co-occurence, median interval, various confidence intervals, other indices of affinity, etc.",
      "topics": [
        "affinity"
      ]
    },
    {
      "page": "affinity2by2",
      "title": "Maximum likelihood estimate and intervals of alpha, null expectation, p-value and traditional indices from a 2x2 table",
      "topics": [
        "affinity2by2"
      ]
    },
    {
      "page": "AlphInts",
      "title": "Median interval, four confidence intervals, null expectation of cooccurrence count, and p-value",
      "topics": [
        "AlphInts"
      ]
    },
    {
      "page": "Bisect",
      "title": "Bisections for finding a root of a function",
      "topics": [
        "Bisect"
      ]
    },
    {
      "page": "Covrg",
      "title": "Coverage Probabilities for Confidence Intervals about alpha, for fixed true alpha",
      "topics": [
        "Covrg"
      ]
    },
    {
      "page": "dataprep",
      "title": "Occurrence matrix (e.g., species by site) data preparation for affinity() function",
      "topics": [
        "dataprep"
      ]
    },
    {
      "page": "EHypMidP",
      "title": "Quantile of the Extended Hypergeometric distribution approximated by the midP distribution function",
      "topics": [
        "EHypMidP"
      ]
    },
    {
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      "title": "Interval of alpha values for which X is a specified q'th quantile",
      "topics": [
        "EHypQuInt"
      ]
    },
    {
      "page": "finches",
      "title": "Darwin’s finches presence–absence data",
      "topics": [
        "finches"
      ]
    },
    {
      "page": "logLikExtHyp",
      "title": "log of Extended Hypergeometric Likelihiood at (X, mA,mB,N, alpha)",
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        "logLikExtHyp"
      ]
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        "MaxX.Int"
      ]
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        "midP.EHyp"
      ]
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        "minmaxAlpha.pFNCH"
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      "topics": [
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      ]
    },
    {
      "page": "plotgg",
      "title": "Heatmap plot of affinity() output",
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      ]
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