{ "_id": "6ae6f84e818c9e3ef6dbb5a3", "Package": "treeSS", "Type": "Package", "Title": "Tree-Spatial Scan Statistic for Cluster Detection", "Version": "0.2.9", "Authors@R": "c(\nperson(\"Allan\", \"Quadros\", email = \"allanvcq@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3250-5380\")),\nperson(\"Andre L. F.\", \"Cançado\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-7019-8521\"))\n)", "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. The method extends Kulldorff\n(1997) circular spatial scan\nstatistic and the tree-based scan statistic of Kulldorff et al.\n(2003) 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)", "URL": "https://github.com/allanvc/treeSS", "BugReports": "https://github.com/allanvc/treeSS/issues", "SystemRequirements": "GNU make", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-11-01 08:23:58 UTC", "User": "root" }, "Author": "Allan Quadros [aut, cre] (ORCID:\n), Andre L. F. Cançado\n[aut] (ORCID: )", "Maintainer": "Allan Quadros ", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "make", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-10-02 18:33:39 UTC", "RemoteUrl": "https://github.com/cran/treeSS", "RemoteRef": "HEAD", "RemoteSha": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "_user": "cran", "_type": "src", "_file": "treeSS_0.2.9.tar.gz", "_fileid": "https://r2.ropensci.org/d3e54c58f18090d4cdf2220f06d9f53cb74100258d5639335642e741c34abfc3", "_filesize": 1256910, "_sha256": "d3e54c58f18090d4cdf2220f06d9f53cb74100258d5639335642e741c34abfc3", "_expires": "2027-02-09T08:29:00.000Z", "_created": "2026-11-01T08:23:58.000Z", "_published": "2026-11-01T08:29:02.391Z", "_upstream": "https://github.com/cran/treeSS", "_status": "success", "_maintainer": { "name": "Allan Quadros", "email": "allanvcq@gmail.com", "login": "allanvc", "orcid": "0000-0003-3250-5380", "description": "Statistician, Instructor of IS/OM at UNF.", "uuid": 19999760 }, "_jobs": [ { "job": 124795349254, "time": 106, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "13076675772" }, { "job": 124795349287, "time": 134, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13076730172" }, { "job": 124795349198, "time": 109, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "13076048283" }, { "job": 124795349251, "time": 128, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "13075384951" }, { "job": 124794505869, "time": 237, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "13076097912" }, { "job": 124795349153, "time": 102, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13076352292" }, { "job": 124795349260, "time": 249, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "13076093608" }, { "job": 124795349256, "time": 148, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13076217836" }, { "job": 124795349311, "time": 208, "config": "windows-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13076292873" }, { "job": 124795349301, "time": 102, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13076601984" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242", "_commit": { "id": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "author": "Allan Quadros ", "committer": "cran-robot ", "message": "version 0.2.9\n", "time": 1790966019 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.0", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "sf", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-20", "n": 1 }, { "week": "2026-22", "n": 1 }, { "week": "2026-27", "n": 1 }, { "week": "2026-28", "n": 1 }, { "week": "2026-31", "n": 1 }, { "week": "2026-40", "n": 1 } ], "_tags": [ { "name": "0.1.44", "date": "2026-05-15" }, { "name": "0.1.50", "date": "2026-05-30" }, { "name": "0.2.4", "date": "2026-07-02" }, { "name": "0.2.5", "date": "2026-07-11" }, { "name": "0.2.6", "date": "2026-07-28" }, { "name": "0.2.9", "date": "2026-10-02" } ], "_stars": 0, "_contributors": [ { "user": "allanvc", "count": 6, "uuid": 19999760 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 635, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 419, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/treeSS" }, "_devurl": "https://github.com/allanvc/treess", "_searchresults": 3, "_topics": [ "cpp", "openmp" ], "_abi": { "exports": [], "imports": [ { "key": "Rcpp::Rcpp_precious_preserve()", "hash": "33a97ea62b293da6" }, { "key": "Rcpp::Rcpp_precious_remove()", "hash": "63d26947ba7e1377" }, { "key": "Rcpp::dataptr()", "hash": "54e69ad2e6668c83" }, { "key": "Rcpp::demangle()", "hash": "b0cfd6754c5ebc4e" }, { "key": "Rcpp::enterRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::exitRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::rcpp_get_stack_trace()", "hash": "c684a9bbe15cdc52" }, { "key": "Rcpp::rcpp_set_stack_trace()", "hash": "33a97ea62b293da6" } ] }, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/treeSS.html" ], "_homeurl": "https://github.com/allanvc/treess", "_realowner": "allanvc", "_cranurl": false, "_releases": [ { "version": "0.1.44", "date": "2026-05-15" }, { "version": "0.1.50", "date": "2026-05-30" }, { "version": "0.2.4", "date": "2026-07-02" }, { "version": "0.2.5", "date": "2026-07-11" }, { "version": "0.2.6", "date": "2026-07-28" }, { "version": "0.2.9", "date": "2026-10-02" } ], "_exports": [ "aggregate_tree", "build_zones", "circular_scan", "filter_clusters", "generate_example_data", "get_cluster_regions", "most_likely_cluster", "pvalue", "secondary_clusters", "sequential_scan", "tree_scan", "treespatial_scan" ], "_datasets": [ { "name": "chicago_crimes", "title": "Chicago Crime (2023)", "object": "chicago_crimes", "class": [ "data.frame" ], "fields": [ "region_id", "area_number", "name", "population", "x", "y", "node_id", "cases", "pop_residential" ], "rows": 30843, "table": true, "tojson": true }, { "name": "chicago_map", "title": "Chicago Community Area Boundaries", "object": "chicago_map", "class": [ "sf", "data.frame" ], "fields": [ "NAME", "AREA_NUM", "geometry" ], "rows": 77, "table": false, "tojson": true }, { "name": "chicago_tree", "title": "Chicago Crime - Hierarchy", "object": "chicago_tree", "class": [ "data.frame" ], "fields": [ "node_id", "parent_id" ], "rows": 2841, "table": true, "tojson": true }, { "name": "fl_deaths", "title": "Florida General Mortality Data (2016)", "object": "fl_deaths", "class": [ "data.frame" ], "fields": [ "county_fips", "county_name", "icd10_code", "icd10_desc", "deaths", "population" ], "rows": 3066, "table": true, "tojson": true }, { "name": "london_boroughs_map", "title": "London Borough Boundaries", "object": "london_boroughs_map", "class": [ "sf", "data.frame" ], "fields": [ "NAME", "GSS_CODE", "geometry" ], "rows": 33, "table": false, "tojson": true }, { "name": "london_collisions", "title": "London Road Collisions (2022)", "object": "london_collisions", "class": [ "data.frame" ], "fields": [ "region_id", "borough", "population", "x", "y", "node_id", "cases" ], "rows": 1546, "table": true, "tojson": true }, { "name": "london_tree", "title": "London Road Collisions - Hierarchy", "object": "london_tree", "class": [ "data.frame" ], "fields": [ "node_id", "parent_id" ], "rows": 81, "table": true, "tojson": true }, { "name": "rj_map", "title": "Rio de Janeiro Municipal Boundaries", "object": "rj_map", "class": [ "sf", "data.frame" ], "fields": [ "ibge_code", "NAME", "geometry" ], "rows": 92, "table": false, "tojson": true }, { "name": "rj_mortality", "title": "Rio de Janeiro Infant Mortality (2016)", "object": "rj_mortality", "class": [ "data.frame" ], "fields": [ "region_id", "ibge_code", "name", "population", "live_births", "x", "y", "node_id", "cases" ], "rows": 1440, "table": true, "tojson": true }, { "name": "rj_tree", "title": "Rio de Janeiro Infant Mortality - ICD-10 Tree", "object": "rj_tree", "class": [ "data.frame" ], "fields": [ "node_id", "parent_id" ], "rows": 622, "table": true, "tojson": true } ], "_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" ] } ], "_readme": "https://github.com/cran/treeSS/raw/HEAD/README.md", "_rundeps": [ "Rcpp" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "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 04:31:00", "modified": "2026-10-02 18:33:39", "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": "2026-05-15 21:32:39", "modified": "2026-10-02 18:33:39", "commits": 4 } ], "_score": 3.778151250383644, "_indexed": false, "_nocasepkg": "treess", "_universes": [ "cran" ], "_indexurl": "https://allanvc.r-universe.dev/treeSS", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.9", "date": "2026-11-01T08:25:52.000Z", "distro": "resolute", "arch": "aarch64", "commit": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "fileid": "https://r2.ropensci.org/fededbfc6f39c6922e64049dfe3b9ad16a4b3265eec0216ff1c8164c2641091c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242" }, { "r": "4.7.0", "os": "linux", "version": "0.2.9", "date": "2026-11-01T08:26:16.000Z", "distro": "resolute", "arch": "x86_64", "commit": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "fileid": "https://r2.ropensci.org/41bf30d07aafc29ae05561778b44176c0b4f10b03107343af383f5e50f378d73", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242" }, { "r": "4.6.1", "os": "linux", "version": "0.2.9", "date": "2026-11-01T08:25:57.000Z", "distro": "resolute", "arch": "aarch64", "commit": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "fileid": "https://r2.ropensci.org/00f577283fd400d39b274d25d8d20272b188b11ad1be2e6a2ec8d9088b0fa501", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242" }, { "r": "4.6.1", "os": "linux", "version": "0.2.9", "date": "2026-11-01T08:26:12.000Z", "distro": "resolute", "arch": "x86_64", "commit": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "fileid": "https://r2.ropensci.org/79a7a8565f7ad8dbbaad57cccdc608f2701fe6a9d2d64ac892e73f328be53936", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.9", "date": "2026-11-01T08:26:07.000Z", "arch": "emscripten", "commit": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "fileid": "https://r2.ropensci.org/663e04b318e6990718e6c89bf60169c0d50f8cb73f7bc32abf3907911f5d899c", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242" }, { "r": "4.7.0", "os": "win", "version": "0.2.9", "date": "2026-11-01T08:27:51.000Z", "arch": "aarch64", "commit": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "fileid": "https://r2.ropensci.org/c3196a15aabd26762a0b01d3d9485dd63e78f7d7342d757ee7d82d880ab37ade", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242" }, { "r": "4.7.0", "os": "win", "version": "0.2.9", "date": "2026-11-01T08:25:19.000Z", "arch": "x86_64", "commit": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "fileid": "https://r2.ropensci.org/21ffdb0e34425c4d6f95531d0702755d94af86daa841c85593d1a6106730ebb2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242" }, { "r": "4.6.2", "os": "win", "version": "0.2.9", "date": "2026-11-01T08:27:15.000Z", "arch": "aarch64", "commit": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "fileid": "https://r2.ropensci.org/ffb4df501388e4a8f9a15b82f804c94fade9f1799d1151c14d41725d405e43bf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242" }, { "r": "4.6.2", "os": "win", "version": "0.2.9", "date": "2026-11-01T08:25:22.000Z", "arch": "x86_64", "commit": "882b204ab7ed1f7dfab3ee715f2df90afc7df441", "fileid": "https://r2.ropensci.org/6ba9ae5bd9fe85b34d17a47b2ad8233cc78abbd55aec1fde724d2f3fad31eff5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/41288339242" } ] }