# HMP/U01 coarsened graph provenance

This directory contains the exact input tables and precomputed layout results
used for the coarsened HMP/U01 giant-component graph shipped with `grip`. The
same files are included in the R Journal reproduction supplement, so the graph
object and paper tables do not depend on an inaccessible project directory.

Source workflow:

- upstream analysis project: `ZB/chm_paper`
- upstream dataset: publicly available HMP+U01 16S amplicon data
- upstream branch: `>=1%` feature screen with `relative_abundance_pca`
- selected graph parameter: `k = 3`
- upstream usable sample count on this branch: `6521`
- original graph giant component size: `6474`
- coarsening trajectory: `6474 -> 3449 -> 1828`

Bundled files:

- `coarse_graph_edges.tsv.gz`: weighted undirected edge list on the coarsened graph
- `coarse_vertex_labels.tsv.gz`: coarse-vertex labels and aggregated metadata
- `coarse_membership.tsv.gz`: exact mapping from original giant-component samples to supernodes
- `coarsening_rounds.tsv`: vertex counts after each coarsening round
- `vignette_results.rds`: candidate summaries and coordinates used by the
  real-data vignette and R Journal paper

The packaged data object `hmp.u01.gc.coarse` is generated from these raw files
by `data-raw/hmp_u01_gc_coarse.R`. The precomputed candidate results are
generated by `inst/scripts/precompute-hmp-results.R`. Both scripts are copied
into the R Journal reproduction supplement.

The bundled tables begin at the coarsened-graph stage: they reproduce the exact
graph, labels, original-to-coarse membership, and reported coarsening trajectory
used in the paper. They do not independently reconstruct the earlier HMP+U01
amplicon processing and iKNN graph-selection workflow.

## SHA-256 checksums

```text
00fade4b8dd58efc5c6609522a87451f8833ef4ee91fdbbaa42cef2f337ae62e  coarse_graph_edges.tsv.gz
95f1a1b97834d3bcb2b9f457f4a4a338fb99837d3f123006aec1f5b289034244  coarse_membership.tsv.gz
a4e1fe85e0ed2778a6dfac619a43b5421de8d373333f6994190ca5bf660134be  coarse_vertex_labels.tsv.gz
27a344f344c2abab8b22ff1b35b70f56c26de9525626aa45258fce836cb4c0d8  coarsening_rounds.tsv
dcbca7c4ada19786929796b1a9d4d8c38af0b9701b03ac18a482e84c9cfed5a9  vignette_results.rds
```
