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CLAUDE.md — SoilUnitAnalysis

Lab Principles Source

  • Repository: EcosystemEcologyLab/lab-principles
  • Commit: 41dd83436ad1bd15520659f0969b64e147ae3e15
  • Copied: 2026-05-11
  • SCIENCE_PRINCIPLES.md v1.0
  • SCIENCE_PRINCIPLES_PIPELINES.md v1.0
  • SCIENCE_PRINCIPLES_TEXT_ANALYSIS.md — NA

Project Context

This project combines soil units mapped and described by the NRCS and remotely- sensed data to describe spatial patterns in plant species distribution and traits on the Santa Rita Experimental Range.The aim of this analysis is to relate soil physical and chemical properties to vegetation distribution and productivity on at scales larger than the site-level.

PI: David Moore, University of Arizona
Collaborators: NA Funding: NA
Repository: https://github.com/EcosystemEcologyLab/SoilUnitAnalysis

Hard Rules — Read These First

1. Data sources

Key data sources include SoilWeb (Web Soil Survey) data and NEON AOP products.

2. Credentials and secrets

All credentials must be read from environment variables. Never hard-code any credential, API key, password, or token. See .env.example for the full list of required environment variables.

3. Data files

The following directories are gitignored and must never be committed: [LIST GITIGNORED DATA DIRECTORIES e.g. data/raw/, data/processed/]

The following directories are git-tracked: [LIST TRACKED DIRECTORIES e.g. data/snapshots/, data/overrides/]

4. [ADD PROJECT-SPECIFIC HARD RULES AS NEEDED]

Environment Variables

Variable Purpose Default
[VARIABLE_NAME] [Purpose] [Default or "required"]

Pipeline Execution Order

[01_script.R]   → [What it does]
[02_script.R]   → [What it does]

Coding Conventions

Language and style

  • Primary language: R
  • [Add style guide reference e.g. tidyverse style guide URL]
  • [Add pipe preference e.g. use base R pipe |> not %>%]

Package preferences

  • [List preferred packages for data manipulation, plotting, etc.]
  • Do not introduce new package dependencies without discussion

Functions

  • Every function must have documentation (roxygen2 for R, docstrings for Python)
  • Every function must have at least one test

QC and Quality Standards

[DESCRIBE QC APPROACH AND THRESHOLDS]

Confidence and Quality Vocabulary

[ADOPT OR DEFINE CONFIDENCE VOCABULARY]

Output Metadata

[DESCRIBE OUTPUT METADATA FORMAT]

Exclusion Logging

[DESCRIBE EXCLUSION LOG LOCATION AND FORMAT]

Known Pending Items

Item Tracked in
[Description] [GitHub issue URL]

Data Use and Citation

[LIST REQUIRED CITATIONS AND DATA USE OBLIGATIONS]