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Add Jaccard signature similarity protocol - #45
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lwaldron merged 4 commits intoOct 18, 2026
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🟡 Changes recommended
Conflicting singleton-matrix instructions and incorrect citation provenance need correction.
3 open issues
What changed in this PR
Adds an atomic protocol for comparing microbial signatures using Jaccard similarity after harmonizing taxa to one rank, addressing issue #8.
Changes:
- Defines harmonization, deduplication, and minimum-length filtering.
- Specifies pair eligibility, matrix layout, and provenance requirements.
- Keeps clustering and visualization outside the protocol’s scope.
| File | Description |
|---|---|
| protocols/jaccard-signature-similarity/protocol.md | Adds the Jaccard similarity procedure, parameters, and output conventions. |
Review effort: Balanced
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| similarity involving an ineligible signature. If fewer than two signatures | ||
| remain, output an empty matrix with its dimensions and reason rather than | ||
| inventing pairwise values. |
| license: CC-BY-4.0 | ||
| type: atomic | ||
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| protocol_citation: "10.1111/j.1469-8137.1912.tb05611.x" |
| type: atomic | ||
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| protocol_citation: "10.1111/j.1469-8137.1912.tb05611.x" | ||
| method_origin_citation: "10.1111/j.1469-8137.1912.tb05611.x" |
Also define the singleton case as a labeled 1 by 1 matrix, note that dissimilarity is 1 - J for consumers that need it, and move the evaluation note out of the protocol. Drafted with Claude Code.
Drafted with Claude Code.
lwaldron
approved these changes
Oct 18, 2026
| every input taxon to the selected rank. | ||
| - **Parameters** | ||
| - `taxonomic_rank`: exactly one rank at which every signature is compared. The | ||
| default is `genus`, matching the worked Jaccard analysis in the source |
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No reason for genus to be a default, would make more sense to default to whatever the most common taxonomic rank is.
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Closes #8
Adds an atomic protocol for calculating pairwise Jaccard similarity between
microbial signatures after harmonizing them to a single taxonomic rank.
The protocol defines: