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    {
      "page": "spaa-package",
      "title": "SPecies Association Analysis",
      "topics": [
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        "spaa"
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      "title": "Compute species' relative frequency",
      "topics": [
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      "title": "Niche overlap between each pair of species",
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      "title": "Analyzing species association",
      "topics": [
        "sp.assoc"
      ]
    },
    {
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      "title": "Species association between each pair of species",
      "topics": [
        "sp.pair"
      ]
    },
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      "title": "Subset species based on relative frequency",
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    },
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      "title": "A sample dataset s",
      "topics": [
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  "_vignettes": [
    {
      "source": "spaa-vignette.Rmd",
      "filename": "spaa-vignette.html",
      "title": "Calculating species association and niche overlap using the spaa R package",
      "author": "Jinlong Zhang",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. The installation",
        "2. Functions and datasets in spaa",
        "2.1 Main Functions",
        "2.2 Embedded datasets",
        "3. Calculating niche width",
        "3.1 Converting community data into a matrix",
        "3.1.2 Individual-based Field Record Sheet",
        "3.1.2 Plot-based Record Sheet",
        "3.2 Calculating species associations",
        "3.2.1 Species association of the community as a whole",
        "1. Variance of species relative frequency (Equation 1) sigmaTsq:",
        "2. Variance of the number of species (Equation 2) STsq",
        "3. Species' relative frequency (Equation 3) pi",
        "4. Variance ratio (Equation 4) var.ratio",
        "5. The W statistic (Equation 5)",
        "3.2.2 Significance test of inters-pecific associations",
        "1. Yates-corrected chi-square test for significance (Equation 6), see chisq and chisqass",
        "2. V ratio (Equation 7) V",
        "3. Jaccard's index (Equation 8) Jaccard:",
        "4. Ochiai index (Equation 9) Ochiai:",
        "5. Dice Index (Equation 10) Dice:",
        "6. PCC: Point Correlation Coefficient PCC (Equation 11)",
        "7. AC Association coefficient (Equation 12) AC",
        "8. Spearman's rank correlation coefficient Spearman (Equation 15)",
        "9. Pearson's correlation coefficient Pearson (Equation 16)",
        "3.3 Calculating niche width",
        "1. Levins niche width index (Equation 17)",
        "2. Shannon's niche width index (Equation 18)",
        "3.4 Niche overlap",
        "1. Levin's niche overlap index (Equation 19)",
        "2. Schoener's niche overlap index (Equation 20)",
        "3. Petraitis's niche overlap index (Equation 21)",
        "4. Pianka's niche overlap index (Equation 22)",
        "5. Czechanowski's niche overlap index (Equation 23)",
        "6. the simplified Morisita index (Equation 24)",
        "Example:",
        "3.5 Bootstrap of the confidence intervals for niche width",
        "3.6 Visualisation",
        "3.6.1 Semi-matrix plots",
        "3.6.2 Species association network",
        "3.7 Other functions",
        "3.7.1 Obtain the most frequently occurred species in the community matrix",
        "3.7.2 Other useful functions",
        "Acknowledgements",
        "References"
      ],
      "created": "2021-02-08 06:15:17",
      "modified": "2021-03-24 06:20:20",
      "commits": 5
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