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 /

/

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