Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

Source code

github.com/blab/flu-forecasting

Contributors

Latest commits

11 Dec 2020 - Test out alternate titer models Adds ability to select strains by different titer assay types (e.g., HI or FRA), adds a config for a dataset and build to test out this concept, and adds results for titer substitution model cross-immunity and other composite distance-from-consensus metric models.

10 Dec 2020 - Update profile to run jobs on SLURM cluster

30 Nov 2020 - Add notebook to produce data for EMD example

10 Dec 2020 - Merge pull request #3 from blab/consensus-metric Consensus metric

09 Dec 2020 - Add forecast table for delta frequency

Pages

/ manuscript / blog-post /

/ analyses / identify-optimal-lbi-parameters /

/ analyses / projected-frequencies /

/ data / simulations /

/

README

Install pandoc and pandoc-crossref. Compile the blog post to HTML with pandoc.

pandoc \
    --filter pandoc-crossref \
    --filter pandoc-citeproc \
    --bibliography=references.bib \
    --csl chicago-author-date.csl \
    --template template.html \
    -s predicting-seasonal-influenza-evolution.md \
    -o predicting-seasonal-influenza-evolution.html