holobiont
0.1.3Microbiome Analysis Tools
Overview
We provide functions for identifying the core community phylogeny in any microbiome, drawing phylogenetic Venn diagrams, calculating the core Faith’s PD for a set of communities, and calculating the core UniFrac distance between two sets of communities. All functions rely on construction of a core community phylogeny, which is a phylogeny where branches are defined based on their presence in multiple samples from a single type of habitat. Our package provides two options for constructing the core community phylogeny, a tip-based approach, where the core community phylogeny is identified based on incidence of leaf nodes and a branch-based approach, where the core community phylogeny is identified based on incidence of individual branches. We suggest use of the microViz package.
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Health
- OK2026-03-1614 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- ERROR2026-03-1313 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
- OK2026-03-1214 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
- ERROR2026-03-1013 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
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Code
Code & tests
Open call graph →Line coverage
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Tests / Examples
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Functions
39 17 exported
Complexity
7 avg / 38 max
Call network
39 nodes / 58 edges
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People & History
2 releases. Pick two to compare their code metrics; R releases are shown for context.
- RR 4.6.0 released · 2026-04-24
- 0.1.3Latest2025-07-22 · current release
- RR 4.5.0 released · 2025-04-11
- 0.1.22024-10-16
Package metadata
- First published
- 2024-10-16
- Total releases
- 2 / 2 yrs
- License
- GPL-2 OSI
- Download size
- not tracked yet
- Installed size
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- With dependencies
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