AlphaSDM 0.2.0

First CRAN release.

• Model settings are now given per model with params, using Earth Engine’s argument names, for example params = list(gbt = list(shrinkage = 0.01)). This replaces the separate arguments n_trees, shrinkage, svm_cost, knn_k and the rest, which applied to several models at once and could silently override values equal to their defaults. Misspelt settings are now an error.
• Every model uses Earth Engine’s defaults, except the tree counts Earth Engine requires (rf 500, gbt 150) and knn, which uses 15 neighbours because Earth Engine’s single neighbour gives a two-value map. The SVM is now Earth Engine’s default linear classifier, and boosted trees use Earth Engine’s learning rate, which gives better-calibrated probabilities.
• Fixed classification SVMs (C_SVC, NU_SVC) returning inverted scores. Their probability depended on the order of the training rows, which Earth Engine does not preserve; the training table is now sorted before fitting.
• generate_pseudo_absences() now reads pseudo-absences from the same years as the presences, in the same proportions, instead of the latest embedding year. Pass aoi_year to place them all in one year.
• Models are trained on their rows in a fixed order, so retraining (which Earth Engine does for every map tile) gives the same model. Random forests are now exactly reproducible; boosted trees vary by at most about 0.005 inside Earth Engine.
• Simpler arguments: balance_trees is gone (use bg_ratio, default 1, or NULL for every absence), as are persist_classifier, async and options from evaluate_models(), which now requires predict_coords with a year column. generate_map() maps the records’ most common year by default.
• sdm_gee_status() is now gee_tasks() and sdm_clean_assets() is gee_clean_assets(). sdm_verbose() and the exported calculate_cbi() are gone: use suppressMessages(), and the cbi from calculate_classifier_metrics().
• Removed naive Bayes, which discards negative values and so cannot use the signed embeddings.
• The vignette now tests models on the following year’s records.
• Maps download straight from Earth Engine in tiles sized to its 32 MB download limit, fetched two at a time and stitched into one GeoTIFF per model. Google Drive is used only for maps Earth Engine will not compute tile by tile.
• generate_map() computes the ensemble on Earth Engine and accepts aoi = "bbox".
• The Earth Engine Python client is declared with reticulate::py_require(), so reticulate installs it when needed; AlphaSDM no longer installs Python itself and no longer depends on ‘rgee’.
• The saved project ID lives in tools::R_user_dir("AlphaSDM", "config"). clear_gee_credentials() removes it and asks before signing out of Earth Engine.
• Connecting to Earth Engine no longer deletes old temporary assets; use gee_clean_assets().
• A getting-started vignette, vignette("AlphaSDM"), maps saguaro around Tucson from GBIF records.
• Removed unused code, including the remains of built-in cross-validation.