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  "_id": "6a1bdede1d7bb097a0a17bcc",
  "Package": "taxdiv",
  "Title": "Taxonomic Diversity Indices Using Deng Entropy",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(\"Muhammet Murat\", \"Gorgoz\", , \"muratgorgoz350@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6398-0005\")),\nperson(\"Kursad\", \"Ozkan\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-8526-7243\")),\nperson(\"Mehmet Guvenc\", \"Negiz\", role = \"aut\",\ncomment = c(ORCID = \"0009-0008-1507-8712\"))\n)",
  "Description": "Calculates taxonomic diversity indices for ecological\ncommunity data using Deng entropy framework and classical\napproaches (Shannon, Simpson, Clarke & Warwick). Provides\nfunctions for computing taxonomic distinctness, average\ntaxonomic distinctness (AvTD/Delta+), variation in taxonomic\ndistinctness (VarTD/Lambda+), and Deng entropy-based measures\nthat incorporate taxonomic hierarchy information. Includes\ntools for constructing taxonomic trees and computing pairwise\ntaxonomic distances.",
  "License": "MIT + file LICENSE",
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  "BugReports": "https://github.com/mgorgoz/taxonomic-diversity-r/issues",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-31 07:07:04 UTC",
    "User": "root"
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  "Author": "Muhammet Murat Gorgoz [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6398-0005>), Kursad Ozkan [aut]\n(ORCID: <https://orcid.org/0000-0002-8526-7243>), Mehmet Guvenc\nNegiz [aut] (ORCID: <https://orcid.org/0009-0008-1507-8712>)",
  "Maintainer": "Muhammet Murat Gorgoz <muratgorgoz350@gmail.com>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-04-01 11:17:56 UTC",
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    "ozkan_pto_full",
    "ozkan_pto_jackknife",
    "ozkan_pto_resample",
    "ozkan_pto_sensitivity",
    "plot_bubble",
    "plot_funnel",
    "plot_heatmap",
    "plot_iteration",
    "plot_radar",
    "plot_rarefaction",
    "plot_taxonomic_tree",
    "pto_components",
    "rarefaction_taxonomic",
    "shannon",
    "simpson",
    "simulate_td",
    "tax_distance_matrix",
    "vartd"
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        "Family",
        "Order",
        "Class",
        "Phylum",
        "Kingdom",
        "Abundance"
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    {
      "name": "gazi_comm",
      "title": "Example Community Vector: 8 Anatolian Tree Species",
      "object": "gazi_comm",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "gazi_gytk",
      "title": "Example Taxonomy: 8 Anatolian Tree Species",
      "object": "gazi_gytk",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Species",
        "Genus",
        "Family",
        "Order"
      ],
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      "table": true,
      "tojson": true
    }
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    {
      "page": "anatolian_trees",
      "title": "Anatolian Forest Trees: Multi-Site Species Data",
      "topics": [
        "anatolian_trees"
      ]
    },
    {
      "page": "avtd",
      "title": "Average Taxonomic Distinctness (Delta+)",
      "topics": [
        "avtd"
      ]
    },
    {
      "page": "batch_analysis",
      "title": "Batch Analysis from a Single Data Frame",
      "topics": [
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      ]
    },
    {
      "page": "build_tax_tree",
      "title": "Build a Taxonomic Tree from Species Data",
      "topics": [
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      ]
    },
    {
      "page": "compare_indices",
      "title": "Compare All Diversity Indices Side by Side",
      "topics": [
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      ]
    },
    {
      "page": "delta",
      "title": "Taxonomic Diversity Index (Delta)",
      "topics": [
        "delta"
      ]
    },
    {
      "page": "delta_star",
      "title": "Taxonomic Distinctness (Delta*)",
      "topics": [
        "delta_star"
      ]
    },
    {
      "page": "deng_entropy_level",
      "title": "Calculate Deng Entropy at a Single Taxonomic Level",
      "topics": [
        "deng_entropy_level"
      ]
    },
    {
      "page": "gazi_comm",
      "title": "Example Community Vector: 8 Anatolian Tree Species",
      "topics": [
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      ]
    },
    {
      "page": "gazi_gytk",
      "title": "Example Taxonomy: 8 Anatolian Tree Species",
      "topics": [
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      ]
    },
    {
      "page": "ozkan_pto",
      "title": "Calculate Ozkan's Taxonomic Diversity Index (pTO)",
      "topics": [
        "ozkan_pto"
      ]
    },
    {
      "page": "ozkan_pto_full",
      "title": "Full Ozkan pTO Pipeline (Islem 1 + 2 + 3)",
      "topics": [
        "ozkan_pto_full"
      ]
    },
    {
      "page": "ozkan_pto_jackknife",
      "title": "Jackknife Analysis for Ozkan's pTO Index (Islem 1 / Run 1)",
      "topics": [
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      ]
    },
    {
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      "title": "Stochastic Resampling of Ozkan's pTO Index (Islem 2 / Run 2)",
      "topics": [
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      ]
    },
    {
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      "title": "Sensitivity Analysis of Ozkan's pTO Index (Islem 3 / Run 3)",
      "topics": [
        "ozkan_pto_sensitivity"
      ]
    },
    {
      "page": "plot_bubble",
      "title": "Bubble Chart of Species Contributions to Diversity",
      "topics": [
        "plot_bubble"
      ]
    },
    {
      "page": "plot_funnel",
      "title": "Funnel Plot for AvTD/VarTD",
      "topics": [
        "plot_funnel"
      ]
    },
    {
      "page": "plot_heatmap",
      "title": "Plot Taxonomic Distance Heatmap",
      "topics": [
        "plot_heatmap"
      ]
    },
    {
      "page": "plot_iteration",
      "title": "Plot pTO Iteration Results from Run 2 or Run 3",
      "topics": [
        "plot_iteration"
      ]
    },
    {
      "page": "plot_radar",
      "title": "Radar (Spider) Chart for Multi-Community Index Comparison",
      "topics": [
        "plot_radar"
      ]
    },
    {
      "page": "plot_rarefaction",
      "title": "Plot Taxonomic Rarefaction Curve",
      "topics": [
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      ]
    },
    {
      "page": "plot_taxonomic_tree",
      "title": "Plot Taxonomic Tree as a Dendrogram",
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        "plot_taxonomic_tree"
      ]
    },
    {
      "page": "pto_components",
      "title": "Calculate All Eight pTO Components (Convenience Wrapper)",
      "topics": [
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      ]
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    {
      "page": "rarefaction_taxonomic",
      "title": "Taxonomic Diversity Rarefaction",
      "topics": [
        "rarefaction_taxonomic"
      ]
    },
    {
      "page": "shannon",
      "title": "Shannon Diversity Index",
      "topics": [
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      ]
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      "page": "simpson",
      "title": "Simpson Diversity Index",
      "topics": [
        "simpson"
      ]
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      "title": "Simulate Expected AvTD/VarTD Under Random Sampling",
      "topics": [
        "simulate_td"
      ]
    },
    {
      "page": "tax_distance_matrix",
      "title": "Compute Taxonomic Distance Matrix",
      "topics": [
        "tax_distance_matrix"
      ]
    },
    {
      "page": "vartd",
      "title": "Variation in Taxonomic Distinctness (Lambda+)",
      "topics": [
        "vartd"
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  "_readme": "https://github.com/cran/taxdiv/raw/HEAD/README.md",
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      "title": "Clarke & Warwick Taxonomic Distinctness",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What Is Taxonomic Distinctness?",
        "The Taxonomic Distance Matrix",
        "The Four Indices",
        "Delta --- Taxonomic Diversity",
        "Delta* --- Taxonomic Distinctness (abundance-weighted)",
        "AvTD (Delta+) --- Average Taxonomic Distinctness",
        "VarTD (Lambda+) --- Variation in Taxonomic Distinctness",
        "Comparing the Four Indices",
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        "Funnel plot",
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        "What Are Classical Diversity Indices?",
        "Shannon-Wiener Index (H')",
        "The idea",
        "The formula",
        "Key properties",
        "Usage in taxdiv",
        "Bias Correction",
        "Simpson Index",
        "Three variants",
        "Understanding the variants",
        "Shannon vs Simpson: When to Use Which?",
        "The Limitation: Why You Need Taxonomic Indices Too",
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        "From Raw Data to Publication-Ready Results",
        "Step 1: Prepare Your Data",
        "Single community (named vector)",
        "Taxonomic tree",
        "Multiple sites (data frame)",
        "Step 2: Compute All Indices at Once",
        "Single community --- compare_indices()",
        "Multiple sites --- batch_analysis()",
        "Step 3: Run the Full Ozkan Pipeline",
        "Step 4: Visualize Results",
        "Compare communities side by side",
        "Inspect the taxonomic tree",
        "Rarefaction curve",
        "Step 5: Export Results",
        "Save to CSV",
        "Save to Excel",
        "Quick Reference: Which Function to Use?"
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        "Overview",
        "Example Data: Mediterranean Forest Community",
        "Classical Diversity Indices",
        "Taxonomic Distance",
        "Clarke & Warwick Taxonomic Distinctness",
        "Deng Entropy and Ozkan pTO",
        "Convenience wrapper",
        "Comparing Communities",
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        "Species Inclusion Probabilities",
        "Full Pipeline Summary",
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        "Taxonomic Distance Heatmap",
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        "Bubble Chart",
        "Radar Chart (Spider Plot)",
        "Rarefaction Curve",
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      "title": "Ozkan pTO Method: Deng Entropy-Based Taxonomic Diversity",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What Is the Ozkan pTO Method?",
        "From Shannon to Deng: Why a New Entropy?",
        "Deng Entropy at Each Taxonomic Level",
        "The 8 Indices Explained",
        "Weighted vs Unweighted",
        "With vs Without Species-Level Shannon",
        "All Levels vs Max-Informative Levels",
        "Which index to use?",
        "The Three-Run Pipeline",
        "Run 1: Deterministic Calculation",
        "Run 2: Stochastic Resampling (Slicing)",
        "Visualizing Run 2",
        "Run 3: Max-Informative Level Variants",
        "Full Pipeline in One Call",
        "Jackknife Leave-One-Out Analysis",
        "Comparing Communities",
        "References"
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      "modified": "2026-04-01 11:17:56",
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    {
      "source": "giris_rehberi.Rmd",
      "filename": "giris_rehberi.html",
      "title": "taxdiv Paketi Kullanim Rehberi (Turkce)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Bu Paket Ne Ise Yarar?",
        "Ornek Veri: Akdeniz Ormani Toplulugu",
        "Adim 1: Klasik Cesitlilik Indeksleri",
        "Adim 2: Taksonomik Mesafe Matrisi",
        "Adim 3: Clarke & Warwick Taksonomik Ayirt Edicilik",
        "Adim 4: Deng Entropisi ve Ozkan pTO (Islem 1)",
        "max_level parametresi",
        "8 Bilesenli Cikti",
        "Adim 5: Stokastik Yeniden Ornekleme (Islem 2 / Run 2)",
        "Adim 6: Duyarlilik Analizi (Islem 3 / Run 3)",
        "Tur Dahil Etme Olasiliklari",
        "Adim 7: Tam Pipeline (ozkan_pto_full)",
        "Adim 8: Jackknife Yanliliksiz Tahmin",
        "Adim 9: Toplu Analiz (batch_analysis)",
        "Adim 10: Rarefaction (Seyreltme)",
        "Adim 11: Simuelasyon ve Huni Grafigi (Funnel Plot)",
        "Gorsellestime",
        "Taksonomik Agac (Dendogram)",
        "Taksonomik Mesafe Isi Haritasi (Heatmap)",
        "Indeks Karsilastirma (Bar Plot)",
        "Islem 2 Iterasyon Grafigi",
        "Tur Katki Baloncuk Grafigi (Bubble Chart)",
        "Radar Grafigi (Spider Chart)",
        "Seyreltme Egrisi (Rarefaction Curve)",
        "Huni Grafigi (Funnel Plot)",
        "Matematiksel Arka Plan",
        "Shannon Entropisi",
        "Simpson Indeksi",
        "Clarke & Warwick: Taksonomik Ayirt Edicilik",
        "Deng Entropisi",
        "Ozkan pTO Formulu",
        "Adim Adim Hesaplama Ornegi",
        "Veri",
        "Adim 1: Shannon",
        "Adim 2: Taksonomik Mesafe",
        "Adim 3: AvTD (Elle)",
        "Adim 4: Deng Entropisi (Tur Seviyesinde)",
        "Adim 5: Ozkan pTO",
        "Fonksiyon Listesi",
        "Klasik Indeksler",
        "Clarke & Warwick Taksonomik Ayirt Edicilik",
        "Ozkan pTO (Deng Entropisi)",
        "Ozkan pTO Pipeline",
        "Toplu Analiz ve Karsilastirma",
        "Simulasyon ve Rarefaction",
        "Gorsellestime (7 plot tipi)",
        "Yardimci Fonksiyonlar",
        "Veri Setleri",
        "Kaynaklar",
        "Klasik Cesitlilik Indeksleri",
        "Taksonomik Farklilik",
        "Deng Entropisi ve Kanit Teorisi",
        "Ozkan pTO Indeksi",
        "Yanliliksiz Tahmin",
        "Rarefaction (Seyreltme)"
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      "filename": "visualization.html",
      "title": "Visualization Guide",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Quick Reference",
        "1. Taxonomic Tree (Dendrogram)",
        "2. Taxonomic Distance Heatmap",
        "3. Bubble Chart",
        "4. Radar Chart (Spider Plot)",
        "5. Iteration Plot (Run 2)",
        "6. Rarefaction Curve",
        "7. Funnel Plot",
        "Customizing Plots"
      ],
      "created": "2026-04-01 11:17:56",
      "modified": "2026-04-01 11:17:56",
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