spatialAtomizeR 0.2.8

This is a resubmission (v0.2.7) addressing reviewer comments on package quality, documentation, and replication material. Changes include:

• Fixed atom ID column renaming to handle both older sf (which produces ID/ID.1 after raster::intersect()) and newer sf >= 1.0 (which produces ID_1/ID_2). Affected simulate_misaligned_data() and the case example vignette (#issue number if you have one).
• Added \examples{} blocks to all exported functions; slow MCMC-based functions use \dontrun{} while lightweight functions (e.g., simulate_misaligned_data(), get_abrm_model(), gen_correlated_spat(), and all S3 methods for misaligned_data) now have fully executable examples
• Changed vcov.abrm example from \dontrun{} to \donttest{} per CRAN policy for examples that are valid but too slow for routine checking
• Fixed run_abrm() silently writing a PDF to the user’s working directory: changed default of save_plots from TRUE to FALSE; diagnostic plots are now obtained explicitly via plot() on the returned object
• Added plot.misaligned_data() S3 method for spatial data exploration
• Added coef.abrm(), confint.abrm(), fitted.abrm(), waic.abrm(), print.waic_abrm() S3 methods to improve model result inspection without accessing internal object structure directly
• Updated vignette to set eval = TRUE for all simulated-data (Example 1) code chunks so the vignette executes and displays output during build
• Removed redundant library(nimble) call from vignette (nimble is already loaded as a dependency of spatialAtomizeR)
• Fixed man page titles to use title case throughout (e.g., “Print Method for ABRM Objects” instead of “Print method for abrm objects”)

Test environments

• local: macOS/Windows/Linux (R 4.4.0)
• GitHub Actions:
  • ubuntu-latest (R-release, R-devel)
  • windows-latest (R-release)
  • macOS-latest (R-release)
• win-builder (R-devel)
• R-hub (ubuntu-gcc-release)

R CMD check results

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Downstream dependencies

There are currently no downstream dependencies for this package.

Previous submission (v0.2.6)

• Fixed Editor’s comments
• Fixed print() statement causing debug output in console
• Fixed unable to use S3 plot() function bug
• Marked 14 internal helper functions as @keywords internal (no longer exported)
• Fixed vignette errors: removed non-existent function parameters and corrected signatures
• Improved S3 method output formatting
• Enhanced documentation with working code examples
• Added vcov() method for variance-covariance matrices
• Fixed coefficient naming for beta_x and beta_y parameters