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

Source code

github.com/blab/flu-forecasting

Contributors

Latest commits

15 Oct 2020 - Merge pull request #2 from blab/blog-post Add blog post content

15 Oct 2020 - Update blog post html

07 Oct 2020 - Finished table with classes to highlight status

07 Oct 2020 - Clean up references in blog post Use the "et al." abbreviation when there are more than two authors (note custom CSL for pandoc-citeproc and updated pandoc command in the README), added citations for simulation software, and added URLs to all references.

06 Oct 2020 - Finished complete draft of blog post Adds section comparing our two studies and refines the conclusion section.

Pages

/

/ data / simulations /

/ analyses / projected-frequencies /

/ analyses / identify-optimal-lbi-parameters /

/ manuscript / blog-post /

Projected frequencies analysis

Example usage

python scripts/project_frequencies.py \
    dist/augur/builds/flu/auspice/flu_h3n2_ha_2016-2018y_1v_0_tree.json \
    frequencies/flu_h3n2_ha_2016-2018y_1v_0.json \
    model_parameters/2016-2018/1/lbi/0.tab \
    projected_frequencies/flu_h3n2_ha_2016-2018y_1v_0.json \
    2016.1 \
    1.0

Example clade trajectories