NEWS
bean 0.2.0
Major changes
find_env_resolution() no longer uses a geometric "elbow" rule on nearest-
neighbour distances. It now selects a kernel-density bandwidth for each
environmental variable using the Sheather-Jones plug-in estimator (default),
with Silverman and Scott rules also available via the new method argument.
The bandwidth is a statistically defensible choice for the edge length of an
environmental grid cell, and the new implementation is faster and more
robust to ties.
rgl is now a Suggests dependency rather than an Imports. 3-D plots
still work when rgl is installed; otherwise plot.bean_ellipsoid() falls
back to a 2-D view of the first two requested dimensions.
- The S3 method
predict.bean_ellipsoid() is now documented under its
canonical name (previously the help page was generated as
predict.ellipsoid_bean).
- Vignettes have been reorganised:
bean-overview — quickstart introduction.
data-preparation — preparing rasters and occurrences.
environmental-thinning — resolution selection and thinning.
niche-modeling — fitting ellipsoids and projecting suitability.
All vignettes now build without requiring rgl.
CRAN readiness
DESCRIPTION: trimmed Imports to MASS, stats, terra; moved rgl,
ggplot2 and dplyr to Suggests (with dplyr removed entirely from the
package — it was only used in one vignette).
- Added a
tests/testthat/ test suite covering find_env_resolution(),
thin_env_nd(), thin_env_center(), fit_ellipsoid() and
predict.bean_ellipsoid().
- Datasets are now documented as user-visible (not
\keyword{internal}).
- Replaced
\dontrun{} examples that depended on missing files with
\donttest{} examples that use the shipped sample data.
prepare_bean() now uses match.arg() for transform.
- Cleaned up
R/globals.R (was carrying many unused identifiers).
Minor
print.bean_ellipsoid() output reformatted for clarity.
- Internal helper
.bean_ellipse_polygon() consolidates the 2-D ellipse
polygon code path used by both fit_ellipsoid() and plot.bean_ellipsoid().
bean 0.1.2
- Earlier development versions; see commit history on GitHub.