Epiverse-TRACE How-to guides

The Epiverse-TRACE How-to guides aim to collect recipe-like reproducible scripts to complete specific Outbreak analytics tasks following concrete steps using R packages. ¹

Describe case data

Title
How to plot age-stratified incidence data by month from date of birth?

Quantify transmission

Title
How to estimate R and k from cluster size data using Markov chain Monte Carlo?
How to estimate R and relative susceptibility from age-stratified pre- and post-epidemic serological data?
How to estimate the effective reproductive number (R_eff) with heterogeneity in social contact?
How to quantify the time-varying reproduction number (R_t)?

Reconstruct transmission

Title
How to reconstruct infection dynamics from incidence data on delayed outcomes like deaths

Create short-term forecast

Title
How to project the future trajectory of the outbreak?

Estimate severity

Title
How to estimate a delay-adjusted age-stratified case fatality risk?

Simulate transmission scenarios

Title
How to create heterogeneous susceptibility matrices?
How to simulate the final size with heterogeneity in social contact and infection susceptibility?
How to use epidemics classes with odin-generated models

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Footnotes

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