Changes in version 0.2.8 (2026-03-24)                  

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