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. Visualise the clusters | Recap | References
Package: treeSS 0.2.4
Allan Quadros
treeSS: Tree-Spatial Scan Statistic for Cluster Detection
Implements the tree-spatial scan statistic for detecting clusters that combine both spatial and hierarchical structures, as proposed by Cancado et al. (2025) <doi:10.1007/s10651-025-00670-w>. The method extends Kulldorff (1997) <doi:10.1080/03610929708831995> circular spatial scan statistic and the tree-based scan statistic of Kulldorff et al. (2003) <doi:10.1111/1541-0420.00039> by searching for anomalies in both geographic regions and branches of hierarchical trees simultaneously. The package also provides standalone implementations of Kulldorff's circular spatial scan statistic and the tree-based scan statistic. Statistical significance is assessed via Monte Carlo simulation under a Poisson or binomial model, with optional 'OpenMP' parallelization.
Authors:
treeSS_0.2.4.tar.gz
treeSS_0.2.4.zip(r-4.7)treeSS_0.2.4.zip(r-4.6)treeSS_0.2.4.zip(r-4.5)
treeSS_0.2.4.tgz(r-4.6-x86_64)treeSS_0.2.4.tgz(r-4.6-arm64)treeSS_0.2.4.tgz(r-4.5-x86_64)treeSS_0.2.4.tgz(r-4.5-arm64)
treeSS_0.2.4.tar.gz(r-4.7-arm64)treeSS_0.2.4.tar.gz(r-4.7-x86_64)treeSS_0.2.4.tar.gz(r-4.6-arm64)treeSS_0.2.4.tar.gz(r-4.6-x86_64)
treeSS_0.2.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
treeSS/json (API)
| # Install 'treeSS' in R: |
| install.packages('treeSS', repos = c('https://allanvc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/allanvc/treess/issues
Datasets:
- chicago_crimes - Chicago Crime
- chicago_map - Chicago Community Area Boundaries
- chicago_tree - Chicago Crime - Hierarchy
- fl_deaths - Florida General Mortality Data
- london_boroughs_map - London Borough Boundaries
- london_collisions - London Road Collisions
- london_tree - London Road Collisions - Hierarchy
- rj_map - Rio de Janeiro Municipal Boundaries
- rj_mortality - Rio de Janeiro Infant Mortality
- rj_tree - Rio de Janeiro Infant Mortality - ICD-10 Tree
Last updated from:4e3923092c. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 164 | ||
| linux-devel-x86_64 | OK | 146 | ||
| source / vignettes | OK | 203 | ||
| linux-release-arm64 | OK | 145 | ||
| linux-release-x86_64 | OK | 141 | ||
| macos-release-arm64 | OK | 111 | ||
| macos-release-x86_64 | OK | 261 | ||
| macos-oldrel-arm64 | OK | 112 | ||
| macos-oldrel-x86_64 | OK | 247 | ||
| windows-devel | OK | 113 | ||
| windows-release | OK | 115 | ||
| windows-oldrel | OK | 124 | ||
| wasm-release | OK | 144 |
Exports:aggregate_treebuild_zonescircular_scanfilter_clustersgenerate_example_dataget_cluster_regionssequential_scantree_scantreespatial_scan
Dependencies:Rcpp
Building treeSS inputs from raw data: Florida mortality 2016
Last update: 2026-07-01
Started: 2026-05-30
Introduction to treeSS: reproducing Cançado et al. (2025)
Overview | Infant mortality in Rio de Janeiro | Run the scan | Why the joint scan matters here | Multiple distinct clusters (paper-faithful) | Visualising the cluster | Secondary clusters when the MLC shadows weaker ones | When to use which | Computational notes | Other examples shipped with the package | References
Last update: 2026-07-01
Started: 2026-04-30
