Protocol: Bray-Curtis dissimilarity matrix between samples
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 48/100
- Issue type
- Documentation
- Clarity
- Mostly clear
- Activity status
- Active
- Domain
- documentation
Research direction
Start by reading the PERMANOVA (#32) and ANOSIM (#33) protocol requirements so the distance-matrix layout will work unchanged for both. Then specify the input scale, normalization choice, formula, zero-total and missing-value handling, and the recorded library call; cite Bray and Curtis 1957 as the origin. Done means the protocol documents these choices and both downstream protocols can consume its stated matrix layout.
Written by the indexing model from the issue text.
Description
Tier: D (cMD paper) · Type: atomic · Category: Statistical Analysis
What
Calculate pairwise Bray-Curtis dissimilarity between all samples in a feature-by-sample abundance table. Output: a sample-by-sample distance matrix with a documented layout.
Why it matters
It is the beta-diversity measure used in the cMD paper and the input to PERMANOVA (#32) and ANOSIM (#33). Splitting it out lets those tests take any distance matrix.
Source material
- Applied in: Manghi et al., Nat Commun 2025, 10.1038/s41467-025-66888-1. Cite this only as an application.
Scope
In: the input scale and whether samples are normalized to proportions first; the formula; treatment of zero-total samples and missing values; the output matrix layout so #32 and #33 consume it unchanged; what is recorded, including the library call used.
Out: other distances; ordination; testing; clustering.
Frontmatter starting point
type: "atomic"
category: "Statistical Analysis"
method_origin_citation: "10.2307/1942268" # Bray and Curtis 1957, verified
tags: [beta-diversity, bray-curtis, distance, microbiome]
Acceptance criteria
- Cites Bray and Curtis 1957 as origin
- Normalization before calculation is a stated, recorded choice
- Output layout is specified so the PERMANOVA and ANOSIM protocols consume it unchanged
Drafted with Claude Code.
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- 1
- Avg merge
- 8d 10h
- Merged PRs (30d)
- 6
Getting set up
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- Read the contributing guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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