Within and between classroom transmission patterns of seasonal influenza and pandemic management strategies at schools

Source codes accompanying Endo et al. "Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan" and Endo et al. "Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools" (in press).

Main files

src/inference.jl: Script for inference of transmission patterns of seasonal influenza in Matsumoto city
src/simulation.jl: Script for school outbreak simulation
src/outputs_inference.jl Script for plotting inference results
src/clusteringanalysis.jl Analysis of temporal clustering of students' onset dates
src/householdsimulation.jl Model validation by simulated of household-school outbreaks
src/hetLK.jl Function definitions for household likelihood
src/SchoolOutbreak.jl Function and structure definitions for inference and simulation
src/schooloutbreaks_Texas.jl Comparison between empirical (Texas, US) and simulated school outbreak sizes
data/anonymizedstudents.jld2 JLD2 data file containing anonymized data
output/Matsumoto_MCMCsamples.csv Posterior MCMC samples generated by inference.jl

Name		Name	Last commit message	Last commit date
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data		data
output		output
src		src
LICENSE		LICENSE
README.md		README.md