[seananderson]

Thanks for working on this package! This PR was Claude assisted. Summary below:

This branch fixes several places where the comparison and retrospective functions silently changed the model they were meant to reproduce. It also makes the helpers independent of the X/Y column names and of an attached ggOceanMaps, and turns on tests and the vignette in R CMD check. It is merged up to current main (0.1.3), so it includes the model-selection functions.

Main fixes

• Refits keep the original model settings. sdmTMB_retro(), compare_meshes(), sdmTMB_mesh_cv() and compare_surveys() (with compiled_model) now refit from the original sdmTMB() call, as update.sdmTMB() does. Before, settings such as spatial_varying, time_varying, extra_time, weights, priors, share_range, anisotropy and reml were dropped. sdmTMB_mesh_cv() also dropped the offset. The call's arguments are evaluated on the main process so they reach parallel workers.
• Coordinate and time columns are no longer hard-coded. Fitted models use object$spde$xy_cols. compare_surveys() gains xy_cols, and the comparison functions gain coord_multiplier. Time columns not named year now work.
• Index and plot fixes.
  • The reference model is always drawn in black.
  • Index plots no longer give NA colours with more than seven series.
  • Peel order is kept with more than ten peels.
  • predict_args now reaches get_index_split().
  • plot_variance_partitioning() only uses link-scale SDs.
  • The "Terminal-year rel. diff." label replaces the misleading Mohn's rho label.
• Other robustness fixes.
  • Non-integer mesh cutoffs work.
  • A failed reference refit warns instead of erroring.
  • A numeric area vector can be subset per row.
  • Barrier meshes are kept, or you get a warning when they can't be.
  • Failed fits report the real error.
  • Fits that fail sanity() are flagged.
  • Map helpers work when ggOceanMaps is loaded but not attached.
• Bug in the merged model-selection code. sdmTMB_selection() passed the list returned by .setup_parallel() to future::plan(), which corrupted the plan for later parallel calls. It now uses .restore_parallel().

Breaking changes

• sdmTMB_retro(refit_meshes = TRUE) now requires cutoff.
• sdmTMB_retro()'s n_workers defaults to 1 (was nyears). With n_workers = 1 the user's current future::plan() is used.
• The %>% re-export is removed.
• ggplot2 >= 3.5.0 is required.

Dependencies and data

• ggOceanMaps moves from Depends to Suggests, and spatial plots fall back to a plain map without it.
• plyr, magrittr and viridis are dropped.
• A small sebastes_bathy dataset and sebastes_depth() let examples, the vignette and tests avoid the ~85 MB bathymetry download.

CI and tests

• tests/ and vignettes/ are no longer build-ignored, so CI runs the tests and builds the vignette.
• New test-refit.R checks that refits reproduce the original fit and index.
• devtools::check() gives 0 errors, 0 warnings and 0 notes locally.