treeSS

Tree-Spatial Scan Statistic for Cluster Detection

Implements the tree-spatial scan statistic (Cançado et al., 2025), which detects clusters that are anomalous in both geographic space and a hierarchical tree simultaneously. The method searches over circular spatial zones and branches of a classification tree to find regions where observed cases significantly exceed expectations under a Poisson or binomial model, selectable via the model argument.

Installation

# CRAN version
install.packages("treeSS")

# Development version from GitHub
# install.packages("remotes")
remotes::install_github("allanvc/treeSS")

Quick start

library(treeSS)

# Example: London road collisions
data(london_collisions)
data(london_tree)

# The scan functions take a data.frame as the first argument and refer to
# its columns by name. This keeps the choice of denominator,
# coordinates, etc. transparent.
result <- treespatial_scan(
  london_collisions,
  cases       = cases,
  population  = population,
  region_id   = region_id,
  x           = x,
  y           = y,
  node_id     = node_id,
  tree        = london_tree,
  nsim        = 999, seed = 42,
  n_cores     = 4L                 # parallelize the MC over 4 threads
)
print(result)

# Extract cluster membership for visualization
cr <- get_cluster_regions(result, n_clusters = 3, overlap = FALSE)

Included datasets

Dataset	Country	Domain	Regions	Tree
`rj_mortality` + `rj_tree`	Brazil	Infant mortality	92 municipalities	ICD-10 (622 nodes)
`fl_deaths`	USA	General mortality	65 counties	raw (built by user)
`london_collisions` + `london_tree`	UK	Road collisions	33 boroughs	Light x Road x Junction (81 nodes)
`chicago_crimes` + `chicago_tree`	USA	Crime	77 community areas	Type x Description x Location (2841 nodes)
`rj_map`, `london_boroughs_map`, `chicago_map`	Brazil / UK / USA	Polygon boundaries	92 / 33 / 77	–

Key functions

treespatial_scan() — tree-spatial scan (main function)
circular_scan() — Kulldorff’s spatial scan
tree_scan() — tree-based scan
filter_clusters() — non-overlapping secondary clusters (Cançado et al. 2025)
sequential_scan() — sequential adjustment for secondary clusters (Zhang, Assunção & Kulldorff 2010)
get_cluster_regions() — cluster membership for any visualization package

Visualization

The package is visualization-agnostic. get_cluster_regions() returns a data.frame that can be merged with any spatial object for plotting with ggplot2, leaflet, tmap, or any other mapping package. The bundled sf boundary datasets (rj_map, london_boroughs_map, chicago_map) let the examples map clusters without any external boundary download. See vignette("introduction") for worked examples with ggplot2 + rj_map (Brazil), leaflet + tigris (USA), and leaflet + london_boroughs_map (London).

References

Cançado, A. L. F., Oliveira, G. S., Quadros, A. V. C., & Duczmal, L. (2025). A tree-spatial scan statistic. Environmental and Ecological Statistics, 32, 953–978. doi:10.1007/s10651-025-00670-w