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bio-epidemiological-genomics-transmission-inference
Maintainer FreedomIntelligence · Last updated April 1, 2026
Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data. Use when investigating outbreak transmission chains or identifying superspreaders.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-epidemiological-genomics-transmission-inference
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- R: TransPhylo::inferTTree() for Bayesian transmission tree inference.
- Infer who infected whom in my outbreak" → Reconstruct transmission networks from genomic and epidemiological data to identify transmission pairs, superspreaders, and unsampled cases. R: TransPhylo::inferTTree() for Bayesian transmission tree inference.
- tree <- read.nexus('dated_tree.nexus').
Source Doc
Excerpt From SKILL.md
TransPhylo in R
library(TransPhylo)
library(ape)
## Convert to TransPhylo format
ptree <- ptreeFromPhylo(tree, dateLastSample = 2020.5)
## Uses MCMC to sample from posterior distribution
res <- inferTTree(
ptree,
mcmcIterations = 100000,
startNeg = 0.1, # Initial within-host effective population
startOff.r = 2, # Initial R0 estimate
startOff.p = 0.5, # Initial sampling probability
startPi = 0.9, # Initial probability of being sampled
dateT = 2020.6 # End of outbreak observation
)
Use cases
- Use when investigating outbreak transmission chains or identifying superspreaders.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- epidemiological-genomics/phylodynamics - Generate dated trees
- epidemiological-genomics/pathogen-typing - Identify outbreak clones
- data-visualization/interactive-visualization - Visualize transmission
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