grunwaldlab / grunwaldlab/metacoder
consider functions for alpha/beta diversity per taxon
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- Dominant language
- R
- Stars
- 148
- Forks
- 30
- PR merge metrics
- No merged PRs in 30d
Description
Usually, diversity stats compare whole communities. Since there is usually a specific group of organisms being worked on (bacteria, fungi), this is implicty the diversity of a taxon. Therefore, we can abstract this to doing calculations on every taxon, with the value of the "root" being the entire "community". This should be possible using compare_groups and heat_tree_matrix. There might be patterns in specific subtaxa not present in their supertaxa.
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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.
Research direction
Start by reading the existing compare_groups and heat_tree_matrix functionality. Determine how alpha and beta diversity are currently calculated for whole communities, then assess how calculations for every taxon could use the root as the full community. Done should include a defined approach for detecting patterns in subtaxa and supporting the requested calculations.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100