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Address the four items requested in the first-round CRAN review.
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):
\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.Rdprint.iterative_scan.Rdprint.tree_scan.Rdprint.treespatial_scan.Rdsummary.circular_scan.Rdsummary.tree_scan.Rdsummary.treespatial_scan.Rd Reference: https://contributor.r-project.org/cran-cookbook/docs_issues.html#missing-value-tags-in-.rd-filesgenerate_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-seedTesting a a clean R CMD check --as-cran.
\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.get_cluster_regions(). Added
@examples block.@examples block to the roxygen comments.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.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-comments.md file.remotes::install_github("allanvc/treeSS").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 . Each summary doc points
to the matching print doc for the full details.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.
treespatial_scan() for combined spatial and
hierarchical cluster detection.circular_scan() for Kulldorff’s circular
spatial scan statistic.tree_scan() for the tree-based scan
statistic.build_zones(),
aggregate_tree(), filter_clusters().print() and summary() methods for all
scan result classes.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.