PhenoPhaseR: Reproducible processing workflow for interpolating phenological DWD observations

Since v1.2.0, two in-pipeline publish hooks package the intermediate filter variant results and the final PHASE entry-date COGs as self-contained RO-Crate 1.2 deposits with W3C-anchored provenance (PROV-O), dataset descriptors (DCAT 3 / Dublin Core Terms), and quality metadata (DQV with SKOS bridge to ISO 19157-1).

As of v1.3.0, Hook B aggregates the per-(phase, year) intermediate outputs into per-phase multi-band Cloud-Optimised GeoTIFFs (one band per year, named by year) and wide-format per-phase VAM CSVs, reducing the published artefact count from ~896 to 21 files while preserving the per-year ISO 19157-1 quality elements through DQV temporal tagging.

v1.4.0 adds two new published quality artefacts to Hook B (CAL, in-sample BAM model-fit diagnostics; GEM, spatial quantiles of the BSE uncertainty raster), auto-writes a README.md into each crate documenting its validation stance, and generates a self-contained ro-crate-preview.html for browser-based inspection without external tooling.

v1.5.0 restructures the DQV quality metadata: each per-year quality measurement is now a first-class top-level entity in the JSON-LD @graph with its own @id, and the per-phase Datasets reference them by @id only — satisfying JSON-LD's node-reference rule and resolving 33 REQUIRED-severity violations previously reported by roc-validator.

v1.6.0 turns the publish hooks into a multi-crop blueprint: a single shared _crop_specs.R file holds per-crop metadata (DWD Plant ID, binomial, AGROVOC concept URI, Wikidata QID) for seven crops (winter wheat, winter rye, winter barley, winter rapeseed, spring barley, oats, maize), a family-wide creators list with explicit DataCite roles, and a layered keyword scheme; both builders are parametric on this configuration. Domain semantics are added via AGROVOC subject terms (schema:about / dct:subject) with DefinedTerm and DefinedTermSet entities in the @graph, alongside the existing W3C / ISO 19157 vocabulary stack.

v1.6.1 is a patch release fixing a promise already under evaluation: recursive default argument reference crash in the v1.6.0 publish hooks (the parameter crop_spec is renamed to crop to break a self-shadowing default); switching the Hook B (PHASE) deposit to a flat layout by default so downstream pipelines can stream individual multi-band COGs from Zenodo via GDAL's /vsicurl/ without downloading the full deposit; and documenting the intentional Schema.org http:// namespace choice in both builders. No numerical changes from v1.6.0; no changes to the multi-crop blueprint or the AGROVOC integration.

v1.6.2 adds resilient temporal-gap handling so a (phase, year) whose interpolation fails because too few stations survived filtering no longer aborts the run: the filter-variant selector logs the dropped cell and reason to opt_scores/GAPS_<plant>.csv, the interpolation writes a full-extent NA surface instead of calling stop(), and the Hook B publisher detects every all-NA band as an ISO 19157-1 DQ_CompletenessOmission measurement. Every COG remains a complete 32-band cube where band i maps to year i. v1.6.2 also adds sugar beet (DWD plant ID 253, Beta vulgaris ssp. vulgaris var. saccharifera) to the blueprint, bringing the deposit family to eight crops; introduces two optional visualization helpers (plot_phenology_raster_maps.R for a DOY/BSE raster pair over a named AOI, and plot_phenology_window_timeseries.R for an AOI-aggregated phase-window time-series across 1993–2024); corrects the RO-Crate profile claim from Workflow Run Crate to Process Run Crate (the WRROC base profile that the existing CreateAction already satisfies); and suppresses GDAL PAM sidecars (.tif.aux.json, .tif.aux.xml) from the Hook B deposit since their content is already in the COG's TIFF tags. No numerical changes to any output for the existing seven crops.

v1.6.3 removes the AGROVOC controlled-vocabulary subject anchors introduced in v1.6.0 after the hand-curated URIs in _crop_specs.R were found to point at unrelated concepts when resolved against agrovoc.fao.org — e.g. the URI labelled "winter rye" resolved to "sawlogs", the URI labelled "phenology" resolved to "local authorities", the URI labelled "Germany" was a different geographic concept. Only the winter-wheat URI verified correctly. Rather than swap to another vocabulary (Wikidata, GEMET) and inherit the same verification burden — controlled-vocabulary subject anchoring is supposed to prevent exactly the typo-points-at-wrong-concept bug we found — the entire subject-anchor layer is removed. The v1.6.3 deposits use only free-text keywords (indexed by Zenodo, OpenAIRE, BonaRes, and Google Dataset Search) and the GeoNames spatialCoverage URI for subject anchoring; the deposits remain valid RO-Crate 1.2 since schema:about is optional in the profile. v1.6.3 also makes the auto-written PHASE README's gap-handling section build-aware, separating the mechanism description (unchanged across deposits) from a conditional "What this deposit reports" subsection that states whether the gap chain actually fired for the build at hand. Already-published v1.6.1 and v1.6.2 crop deposits retain their original schema:about entries on Zenodo as historical record; the cleanup lands on their next coordinated re-release. No numerical changes to any output, no changes to the publish-hook machinery, the PROV-O lineage, or the DQV quality measurements.

v1.7.0 reinstates the AGROVOC subject layer — this time with every URI verified against agrovoc.fao.org and a build-time guard (verify_agrovoc_uris()) that resolves each URI against the live catalogue and reports any that no longer match the concept they claim. Of the original v1.6.0 set, only winter wheat (c_8412) and maize (c_12332) had been correct; the other seven URIs are corrected (e.g. phenology c_28793 → c_5774, growing degree days c_36099 → c_28c4c002, Germany c_3258 → c_3245). Winter rye and winter rapeseed anchor to the generic species concept because AGROVOC has no winter-specific entry — the season is carried by the DWD Plant ID and the free-text keyword. "Spatial interpolation" has no AGROVOC concept and remains a free-text keyword. PHASE deposits additionally anchor spatial data (c_379bbe9f) and statistical uncertainty (c_28975, for the BSE layer). v1.7.0 also makes all DQV quality measures anchor honestly: schema:propertyID carries the bare measure token rather than a fabricated iso19157:<measure> IRI (no such concepts exist in ISO 19157), with the ISO link made only at the genuine dimension-class level via dqv:inDimension. Finally, v1.7.0 adds a validated prediction-interval calibration of the BSE uncertainty layer (PIC: PICP and MPIW at nominal 90%), computed by a dedicated k-fold cross-validation over all stations, separate from the production all-data fit so the published rasters are never degraded — each station is held out exactly once, and the interval combines each fold's se.fit with the production residual variance. These are surfaced as DQV measurements under DQ_UsabilityElement tied to the BSE COG via dqv:computedOn. This distinguishes what the BSE layer is (a model-internal statistical uncertainty) from how well-calibrated it turned out (a validated coverage statement). No numerical changes to any output. Already-published deposits keep their original encoding as historical record; the existing records pick up the v1.7.0 metadata.