Navigation: Repo Home | Docs Hub | Setup | Shared Scripts | Reproduce | Pipeline Map | Find Data | Join & Query Guide | Data Products
This is the main navigation page for the repository documentation. Use it to move between the high-level overview, exact reproduction steps, technical workflow references, and the code that implements each workstream. The companion Data Products page also documents the minimal server-aligned directory skeleton that is now tracked with .gitkeep placeholders where needed.
| Goal | Go to... |
|---|---|
| Understand the repo at a glance | Repo Home |
| Run the core pipeline to model results | Core pipeline |
| See the current model results | Model runs |
| See the whole pipeline visually | Pipeline Map |
| Reproduce the active production pipelines | Reproduce |
| Find a product or variable | Searchable Data Catalog |
| See how products join or build a dataset | Dataset Query Guide |
| Understand output and storage conventions | Data Products |
| Understand shared climate architecture | Architecture |
| Review QC and validation coverage | Testing and QC |
| Set up the environment | Setup |
| Understand root-level helper scripts | Shared Scripts |
| Understand FIA plot design visually | FIA visual explainer |
| Review the forest data explorer design | Forest Data Explorer Design |
| Review the manuscript-facing consolidated methods | Supplemental methods working draft |
| Review the concise current condition-level definitions | Current analysis methods |
| Find the tree-weighting and understory CWM sensitivities | CWM sensitivity products |
| Use the searchable local dashboard | Dashboard guide |
- Species niche overview
- Species niche technical workflow
- Species niche methods
- Species niche QA guide
- Thermophilization overview (related plot-visit method; not used by the current models)
| Directory | What it covers | Overview | Technical workflow | Scripts |
|---|---|---|---|---|
01_ids/ |
IDS download, cleaning, spatial joins, area metrics | README | WORKFLOW | scripts/ |
02_terraclimate/ |
GEE-based TerraClimate extraction for IDS locations | README | WORKFLOW | scripts/ |
03_prism/ |
PRISM web-service extraction for CONUS IDS locations | README | WORKFLOW | scripts/ |
04_worldclim/ |
WorldClim local GeoTIFF extraction for IDS locations | README | WORKFLOW | scripts/ |
05_fia/ |
FIA plot summaries, disturbance, treatment, and site climate | README | WORKFLOW | scripts/ |
06_species_niches/ |
BIEN range-map and TerraClimate species niches | README | WORKFLOW | scripts/ |
07_thermophilization/ |
Related method: forest community climate affinity per plot visit, change between repeated surveys, and disturbance extent; not used by the current models | README | Output guide | scripts/ |
08_disturbance_linkage/ |
Resource: prepared FIA, MTBS, and IDS disturbance evidence; not used by the current models | README | WORKFLOW | scripts/ |
09_analysis/ |
Core analysis: stable-condition cumulative mortality, climate-niche responses, site CWD, and preliminary models; separate severity pending | README | Methods | Scripts |
archive/05_era5/ |
Archived ERA5 extraction reference and directory layout | README | WORKFLOW | scripts/ |
| Page | Purpose |
|---|---|
| Reproduce | Exact production run order, grouped by workstream |
| Pipeline Map | GitHub-renderable diagram plus links to the dashboard and HTML companion |
| Dataset Query Guide | Safe joins, row expansion, and ready-made query recipes |
| Data Products | Main outputs, tracked review files, local-only artifacts, and server-aligned directory paths |
| Architecture | Shared climate extraction concepts and data model |
| Supplemental methods working draft | Manuscript-facing synthesis of FIA, niches, CWMs, mortality, climate, models, and sensitivities |
| CWM sensitivity products | Commands, outputs, and interpretation for tree weighting and understory diagnostics |
| Testing and QC | Optional diagnostics, validation steps, and known QC gaps |
| FIA visual explainer | Static visual guide to FIA plot design, sampling grain, and FIADB tables |
| Category | Location | Notes |
|---|---|---|
| Production | 01_ids/scripts/ | IDS production and QC scripts |
| Production | 02_terraclimate/scripts/ | TerraClimate production plus exploratory script |
| Production | 03_prism/scripts/ | PRISM production scripts |
| Production | 04_worldclim/scripts/ | WorldClim production scripts |
| Production | 05_fia/scripts/ | FIA production scripts |
| Production | 06_species_niches/scripts/ | Species climate-niche production scripts |
| Related method | 07_thermophilization/scripts/ | Community climate-affinity, disturbance severity, and repeated-survey change scripts |
| Shared | scripts/ | Setup helper, shared climate summary builder, reusable utilities, demos, and test runner |
| Archived | archive/05_era5/scripts/ | ERA5 reference implementation retained outside the active run path |
| Dashboard | docs/dashboard/ | Streamlit app, Query Builder, and launch guide |
- Dashboard guide for launching the searchable catalog and Query Builder locally.
- Pipeline Map for the GitHub-friendly Markdown summary.
- pipeline_diagram.html for a short static HTML companion.