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  "Title": "Tree-Spatial Scan Statistic for Cluster Detection",
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  "Description": "Implements the tree-spatial scan statistic for detecting\nclusters that combine both spatial and hierarchical structures,\nas proposed by Cancado et al. (2025)\n<doi:10.1007/s10651-025-00670-w>. The method extends Kulldorff\n(1997) <doi:10.1080/03610929708831995> circular spatial scan\nstatistic and the tree-based scan statistic of Kulldorff et al.\n(2003) <doi:10.1111/1541-0420.00039> by searching for anomalies\nin both geographic regions and branches of hierarchical trees\nsimultaneously. The package also provides standalone\nimplementations of Kulldorff's circular spatial scan statistic\nand the tree-based scan statistic. Statistical significance is\nassessed via Monte Carlo simulation under a Poisson or binomial\nmodel, with optional 'OpenMP' parallelization.",
  "License": "GPL (>= 3)",
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  "Author": "Allan Quadros [aut, cre]\n(<https://orcid.org/0000-0003-3250-5380>), Andre L. F. Cançado\n[aut] (<https://orcid.org/0000-0002-7019-8521>)",
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    "sequential_scan",
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        "parent_id"
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        "county_name",
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        "population"
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        "data.frame"
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        "GSS_CODE",
        "geometry"
      ],
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      "table": false,
      "tojson": true
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        "population",
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        "cases"
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      "table": true,
      "tojson": true
    },
    {
      "name": "london_tree",
      "title": "London Road Collisions - Hierarchy",
      "object": "london_tree",
      "class": [
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      "fields": [
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        "parent_id"
      ],
      "rows": 81,
      "table": true,
      "tojson": true
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        "geometry"
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        "cases"
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      "rows": 1440,
      "table": true,
      "tojson": true
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        "parent_id"
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      "table": true,
      "tojson": true
    }
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  "_help": [
    {
      "page": "treeSS-package",
      "title": "treeSS: Tree-Spatial Scan Statistic for Cluster Detection",
      "topics": [
        "treeSS-package",
        "treeSS"
      ]
    },
    {
      "page": "aggregate_tree",
      "title": "Aggregate Case Counts from Leaves to All Nodes in a Hierarchical Tree",
      "topics": [
        "aggregate_tree"
      ]
    },
    {
      "page": "build_zones",
      "title": "Build Candidate Spatial Zones Using Circular Windows",
      "topics": [
        "build_zones"
      ]
    },
    {
      "page": "chicago_crimes",
      "title": "Chicago Crime (2023)",
      "topics": [
        "chicago_crimes"
      ]
    },
    {
      "page": "chicago_map",
      "title": "Chicago Community Area Boundaries",
      "topics": [
        "chicago_map"
      ]
    },
    {
      "page": "chicago_tree",
      "title": "Chicago Crime - Hierarchy",
      "topics": [
        "chicago_tree"
      ]
    },
    {
      "page": "circular_scan",
      "title": "Kulldorff's Circular Spatial Scan Statistic",
      "topics": [
        "circular_scan"
      ]
    },
    {
      "page": "filter_clusters",
      "title": "Filter Overlapping Secondary Clusters",
      "topics": [
        "filter_clusters",
        "filter_clusters.circular_scan",
        "filter_clusters.default",
        "filter_clusters.treespatial_scan",
        "filter_clusters.tree_scan"
      ]
    },
    {
      "page": "fl_deaths",
      "title": "Florida General Mortality Data (2016)",
      "topics": [
        "fl_deaths"
      ]
    },
    {
      "page": "generate_example_data",
      "title": "Generate Example Data for Tree-Spatial Scan",
      "topics": [
        "generate_example_data"
      ]
    },
    {
      "page": "get_cluster_regions",
      "title": "Extract Cluster Membership for Each Region",
      "topics": [
        "get_cluster_regions",
        "get_cluster_regions.default",
        "get_cluster_regions.sequential_scan"
      ]
    },
    {
      "page": "london_boroughs_map",
      "title": "London Borough Boundaries",
      "topics": [
        "london_boroughs_map"
      ]
    },
    {
      "page": "london_collisions",
      "title": "London Road Collisions (2022)",
      "topics": [
        "london_collisions"
      ]
    },
    {
      "page": "london_tree",
      "title": "London Road Collisions - Hierarchy",
      "topics": [
        "london_tree"
      ]
    },
    {
      "page": "most_likely_cluster",
      "title": "Extract the Most Likely Cluster from a Scan Result",
      "topics": [
        "most_likely_cluster",
        "most_likely_cluster.sequential_scan",
        "most_likely_cluster.treess"
      ]
    },
    {
      "page": "plot.tree_scan",
      "title": "Plot the Top Tree Cuts of a Tree-Only Scan",
      "topics": [
        "plot.tree_scan"
      ]
    },
    {
      "page": "plot.treess",
      "title": "Plot the Clusters Detected by a Scan",
      "topics": [
        "plot.treess"
      ]
    },
    {
      "page": "print.circular_scan",
      "title": "Print Method for circular_scan Objects",
      "topics": [
        "print.circular_scan"
      ]
    },
    {
      "page": "print.sequential_scan",
      "title": "Print Method for sequential_scan Objects",
      "topics": [
        "print.sequential_scan"
      ]
    },
    {
      "page": "print.tree_scan",
      "title": "Print Method for tree_scan Objects",
      "topics": [
        "print.tree_scan"
      ]
    },
    {
      "page": "print.treespatial_scan",
      "title": "Print Method for treespatial_scan Objects",
      "topics": [
        "print.treespatial_scan"
      ]
    },
    {
      "page": "pvalue",
      "title": "Extract the Monte Carlo P-Value from a Scan Result",
      "topics": [
        "pvalue",
        "pvalue.sequential_scan",
        "pvalue.treess"
      ]
    },
    {
      "page": "rj_map",
      "title": "Rio de Janeiro Municipal Boundaries",
      "topics": [
        "rj_map"
      ]
    },
    {
      "page": "rj_mortality",
      "title": "Rio de Janeiro Infant Mortality (2016)",
      "topics": [
        "rj_mortality"
      ]
    },
    {
      "page": "rj_tree",
      "title": "Rio de Janeiro Infant Mortality - ICD-10 Tree",
      "topics": [
        "rj_tree"
      ]
    },
    {
      "page": "secondary_clusters",
      "title": "Extract Secondary Clusters from a Scan Result",
      "topics": [
        "secondary_clusters",
        "secondary_clusters.sequential_scan",
        "secondary_clusters.treess",
        "secondary_clusters.tree_scan"
      ]
    },
    {
      "page": "sequential_scan",
      "title": "Sequential Scan for Secondary Clusters",
      "topics": [
        "sequential_scan"
      ]
    },
    {
      "page": "summary.circular_scan",
      "title": "Summary Method for circular_scan Objects",
      "topics": [
        "summary.circular_scan"
      ]
    },
    {
      "page": "summary.sequential_scan",
      "title": "Summary Method for sequential_scan Objects",
      "topics": [
        "summary.sequential_scan"
      ]
    },
    {
      "page": "summary.tree_scan",
      "title": "Summary Method for tree_scan Objects",
      "topics": [
        "summary.tree_scan"
      ]
    },
    {
      "page": "summary.treespatial_scan",
      "title": "Summary Method for treespatial_scan Objects",
      "topics": [
        "summary.treespatial_scan"
      ]
    },
    {
      "page": "tree_scan",
      "title": "Tree-Based Scan Statistic",
      "topics": [
        "tree_scan"
      ]
    },
    {
      "page": "treespatial_scan",
      "title": "Tree-Spatial Scan Statistic",
      "topics": [
        "treespatial_scan"
      ]
    }
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      "homepage": "http://gcc.gnu.org/",
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  "_vignettes": [
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      "source": "florida.Rmd",
      "filename": "florida.html",
      "title": "Building treeSS inputs from raw data: Florida mortality 2016",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What this vignette adds",
        "1. Load the raw data",
        "2. Build the ICD-10 tree from the codes in the data",
        "3. Download polygons and centroids",
        "4. Assemble the long-format data.frame",
        "5. Run the tree-spatial scan",
        "6. Distinct secondary clusters (paper-faithful)",
        "7. Sequential scan when the MLC may shadow",
        "8. Visualize the clusters",
        "Recap",
        "References"
      ],
      "created": "2026-05-30 01:37:11",
      "modified": "2026-10-02 15:53:12",
      "commits": 3
    },
    {
      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Introduction to treeSS: reproducing Cançado et al. (2025)",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Infant mortality in Rio de Janeiro",
        "Run the scan",
        "Why the joint scan matters here",
        "Multiple distinct clusters (paper-faithful)",
        "Visualizing the cluster",
        "Secondary clusters when the MLC shadows weaker ones",
        "When to use which",
        "Computational notes",
        "Other examples shipped with the package",
        "References"
      ],
      "created": "2026-04-30 04:02:23",
      "modified": "2026-10-02 15:53:12",
      "commits": 4
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