Protocol: Shannon diversity of a single sample
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 55/100
- Issue type
- Documentation
- Clarity
- Mostly clear
- Activity status
- Active
- Tech stack
- yaml
- Domain
- documentation
Research direction
Start by reading the larger diversity protocol in #43 and the repository’s existing atomic protocols to find the expected format and conventions. Draft a standalone Shannon-index protocol using the supplied frontmatter; define input scale, logarithm default, missing-value handling, and rarefaction or depth-normalization behavior. Done when it cites Shannon 1948 as the origin and meets all four acceptance criteria.
Written by the indexing model from the issue text.
Description
Tier: D (cMD paper) · Type: atomic · Category: Statistical Analysis
What
Calculate the Shannon index for each sample from a feature-by-sample abundance table. Output: one value per sample and nothing more.
Why it matters
Alpha diversity is the first summary computed in nearly every microbiome analysis, and it was bundled into a larger diversity protocol in #43 that review asked to split.
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 (counts or proportions) and conversion to proportions; the logarithm base as a parameter; treatment of zeros and of missing values (error, do not impute); whether and how samples are rarefied to equal depth before calculation, since richness-sensitive indices rise with sequencing depth; what is recorded.
Out: beta diversity; any group comparison or test; interpretation.
Frontmatter starting point
type: "atomic"
category: "Statistical Analysis"
method_origin_citation: "10.1002/j.1538-7305.1948.tb01338.x" # Shannon 1948, verified
tags: [alpha-diversity, shannon, microbiome]
Acceptance criteria
- Cites Shannon 1948 as origin, not a paper that applies it
- Logarithm base is a stated parameter with a default
- Rarefaction or depth normalization has a defined, recorded behaviour
- Missing values stop the calculation rather than being treated as zero
Drafted with Claude Code.
- Dominant language
- No language data
- Stars
- 0
- Forks
- 1
- Avg merge
- 4d 17h
- Merged PRs (30d)
- 6
Getting set up
- No Dockerfile or Docker Compose file
- No pull request template
- 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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