NEWS.md

In treeSS: Tree-Spatial Scan Statistic for Cluster Detection

treeSS 0.1.44

CRAN reviewer feedback

Address the four items requested in the first-round CRAN review.

DESCRIPTION

• Single-quote software/API names per the CRAN cookbook: OpenMP is now written as 'OpenMP' in the package description. Reference: https://contributor.r-project.org/cran-cookbook/description_issues.html#formatting-software-names

• Add DOI links to the two references that were previously cited without a link, using the CRAN-mandated authors (year) <doi:...> form (no space after doi:, no space inside the angle brackets):

  • Kulldorff (1997)
  • Kulldorff et al. (2003) Reference: https://contributor.r-project.org/cran-cookbook/description_issues.html#references

Documentation (R/print.R, R/iterative_scan.R, man/*.Rd)

• Added missing \value tags (and the corresponding @return roxygen blocks) to the seven print()/summary() method Rd files flagged by CRAN. Each documents that the method invisibly returns its input object unchanged and is called for its printing side effect, with a description of the fields written to the console (and, for summary() methods, the additional fields beyond those of the matching print() method):
  • print.circular_scan.Rd
  • print.iterative_scan.Rd
  • print.tree_scan.Rd
  • print.treespatial_scan.Rd
  • summary.circular_scan.Rd
  • summary.tree_scan.Rd
  • summary.treespatial_scan.Rd Reference: https://contributor.r-project.org/cran-cookbook/docs_issues.html#missing-value-tags-in-.rd-files

Bug fixes (R/generate_example_data.R, man/generate_example_data.Rd)

• generate_example_data() no longer sets a hardcoded seed within the function: the default of the seed argument is now NULL (previously 123L). When the user does not pass a seed, the function draws from the user's session-level RNG state without modifying it; when the user passes an explicit integer, the existing save-and-restore logic (introduced in 0.1.43) still applies. The \usage{} block and the \item{seed}{...} description of the corresponding Rd file have been updated to match. The roxygen example (ex <- generate_example_data(seed = 42)) is unchanged: it passes an explicit seed and so remains reproducible. Reference: https://contributor.r-project.org/cran-cookbook/code_issues.html#setting-a-specific-seed

treeSS 0.1.43

CRAN-readiness pass

Testing a a clean R CMD check --as-cran.

DESCRIPTION

• added ORCID from Andre

Documentation (R/data.R, man/{chicago,london,rj}_tree.Rd)

• Added \source{} blocks to all three tree datasets, pointing at the corresponding leaf-level dataset and at the data-raw/ build script in the GitHub repo.

Documentation (R/get_cluster_regions.R, man/get_cluster_regions.Rd)

• Added a worked example to get_cluster_regions(). Added @examples block.

Documentation (R/filter_clusters.R)

• Added an @examples block to the roxygen comments.

Bug fixes (R/circular_scan.R, R/tree_scan.R, R/treespatial_scan.R, R/generate_example_data.R)

• The four functions that accept a seed = ... argument no longer silently overwrite the user's session-level RNG state. Previously, calling treespatial_scan(..., seed = 42) after a set.seed(2026) in the user's session would leave the RNG in a state determined by the internal Monte Carlo loop, so any subsequent runif(), sample(), etc. was no longer reproducible from the user's set.seed(2026). Now the user's pre-existing RNG state is saved on entry and restored on exit (whether the function returns normally or via an error), so the seed argument affects only the result of the call. Implementation is in two new internal helpers .seed_save_and_set() and .seed_restore() in R/utils.R.

Print methods (R/iterative_scan.R, man/print.iterative_scan.Rd)

• print.iterative_scan() now accepts max_show for API consistency with the other three print methods. The default behavior is unchanged (the table is printed without the region_ids and leaf_ids columns to keep it compact); pass max_show = -1L to include both columns.

CRAN submission infrastructure

• Added cran-comments.md file.

README.md

• Updated the install snippet to a CRAN install + a development install via remotes::install_github("allanvc/treeSS").

treeSS 0.1.42

Documentation (R/print.R, man/*.Rd)

• The summary() methods for circular_scan, tree_scan, and treespatial_scan now have proper roxygen descriptions and explicitly document that the max_show argument added in 0.1.39 is forwarded to the corresponding print() method via \code{...}. Each summary doc points to the matching print doc for the full details.

treeSS 0.1.39

Print methods (R/print.R) - truncation by default

The print methods now truncate long Leaf IDs and Regions lists by default, in the style of tibble. The motivation is the Chicago example: the most likely cluster turns out to be the root of the FBI crime taxonomy (1900+ leaves), which under the previous policy printed every single leaf, producing more than 10 pages of console output in the rendered PDF.

• New argument max_show on print.treespatial_scan(), print.tree_scan() and print.circular_scan(). Default is 10L. When a vector field exceeds this length, only the first max_show values are shown and a tail of ... and N more is appended. Pass max_show = -1L (or any value at least as large as the field) to recover the previous full-output behavior.

• The internal .cat_wrapped() helper gained the same max_show argument (default 10L) and propagates it through the print methods.

• No changes to the underlying scan results: only the console / PDF rendering of the result objects is affected. The full leaf and region IDs are always available on result$most_likely_cluster$ leaf_ids and result$most_likely_cluster$region_ids for programmatic use.

The choice of default mirrors tibble's behavior: enough to give the reader a sense of the cluster contents, but not so much that a single print() call dominates the document.

treeSS 0.1.18

• Initial release.
• Implements the tree-spatial scan statistic (Cancado et al., 2025).
• Provides treespatial_scan() for combined spatial and hierarchical cluster detection.
• Provides circular_scan() for Kulldorff's circular spatial scan statistic.
• Provides tree_scan() for the tree-based scan statistic.
• Helper functions: build_zones(), aggregate_tree(), filter_clusters().
• S3 print() and summary() methods for all scan result classes.
• Monte Carlo simulation for p-value computation, with the null resampler matched to the chosen model (multinomial conditional resampling for Poisson; binomial conditional resampling for binomial).

treeSS documentation built on May 16, 2026, 1:08 a.m.