add ca fertilization harmonization and ncc compost support

[divine7022]

Updated description (following review + major revisions)

Description

Adds reproducible California nitrogen-fertilization and organic-amendment reference datasets to PEcAn.data.land.

The PR includes curated source TSVs, harmonization scripts, packaged datasets, lookup functions, documentation, and data-validation checks. It adds:

• ca_n_application_rate
• ca_organic_amendment_properties
• ca_organic_amendment_app_rate

Opinionated priors, samplers, and the proposed ncc event-schema changes were removed; workflow-specific sampling remains downstream in #4003.

Motivation

Moves the previously external harmonization workflow into the repository so the datasets can be reviewed and rebuilt from a clean checkout.

Type of change

• New feature

Checklist

• Documentation updated
• Data provenance and update procedure documented
• Validation checks added
• Dependency metadata regenerated

---

Original description

Description

folds standalone N fertilization harmonization (was living at /projectnb/dietzelab/ccmmf/management/fertilization/harmonization.R) into data.land data-raw pipeline, then layers ncc (compost) sampling support on top and extends the events schema with an ncc event type

events_schema_v0.1.2.json picks up ncc as an allowed event_type with material, ncc_subtype, fert_subtype, and pft properties

separate workflow PR will consume these samplers from workflows/fertilization-statewide and workflows/ncc-statewide to emit ensemble events

cc @sarahkanee @mdietze @infotroph @dlebauer

Motivation and Context

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation.
• My name is in the list of CITATION.cff
• I agree that PEcAn Project may distribute my contribution under any or all of
  • the same license as the existing code,
  • and/or the BSD 3-clause license.
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.

[divine7022]

quick context first, since this turned into a structural change. where we started, the build scripts here were reading the curated fertilization data straight from Mike's team's spreedsheet, and doing the harmonization in place mapping the source URLs to citations, the unit conversions, the property vs rate columns, the material classes. So the .rda we shipped was harmonized version, but all that harmonization logic was baked into package build

per discussion, now I flipped it. harmonization moved out to a standalone harmonize_fertilization_data.R on SCC. It reads original TSVs and writes already harmonized CSVs, those CSVs land in data-raw/, and create_*.R scripts just read them and call use_data(). No curation left in the package, it's purely packaging clean data now. That's the "no manual curation step, provenance is the R script" case you pointed at

regarding docs, rewrote the roxygen for all three datasets, and added a data-raw/README.md covering where the raw sheet comes from, the curation decisions, and how to update

Make sure naming is consistent, e.g. create_n_rate_data.R reads a file n_fertilizaton.tsv and generates a dataset ca_n_application_rate. This can get confusing.

consider renaming compost.tsv to organic_ammendments.tsv to bettr reflect the diversity of materials represented in the dataset.

corrected, and went past the rename. now names lines up: ca_n_application_rate.csv, create_ca_n_application_rate.R, ca_n_application_rate, same for amendments. I have dropped compost.tsv, instead of just renaming it I split it into ca_organic_amendment_properties and ca_organic_amendment_app_rate (more in ^^ thread) and dropped "compost" name since the table's mostly manure, straw, wood chips, paper, blood meal

[dlebauer]

A few requests on writing style left as comments and as Slack DM.

[mdietze]

@dlebauer @infotroph would be great to get this through review so we can get 4003 (which depends on this) and 4050 (which depends on 4003) reviewed as well

[dlebauer]

Requested changes have been substantially addressed. Thank you for your work on this and patience with the review!

Requested changes have been implemented in subsequent commits, including removal of the opinionated priors and samplers and separation of amendment properties from application rates. Dismissing this review as outdated.