├── .gitignore ├── README.md ├── Rakefile ├── correspondence ├── cover_letter.tex ├── reresponse.tex └── response.tex ├── data ├── H1N1_HI_data.tsv ├── H1N1_sample.trees ├── H1N1_seq_data.tsv ├── H3N2_HI_data.tsv ├── H3N2_sample.trees ├── H3N2_seq_data.tsv ├── Vic_HI_data.tsv ├── Vic_sample.trees ├── Vic_seq_data.tsv ├── Yam_HI_data.tsv ├── Yam_sample.trees ├── Yam_seq_data.tsv └── incidence_data.tsv ├── example-xmls ├── H1N1_mds_drift_effects_notree.xml ├── H1N1_mds_drift_effects_tree.xml ├── H1N1_mds_drift_noeffects_notree.xml ├── H1N1_mds_nodrift_noeffects_notree.xml ├── H3N2_mds_drift_effects_tree.xml ├── README.md ├── Vic_mds_drift_effects_tree.xml └── Yam_mds_drift_effects_tree.xml ├── figure-data ├── README.md ├── fig02_fig03_mds.tsv ├── fig05_year_to_year_drift.tsv ├── fig09_smith_mds.tsv ├── fig10_smith_mds_rotation.tsv ├── fig11_smith_mds_drift.tsv └── fig12_smith_mds_effects.tsv ├── figures ├── corr.png ├── counts_corr.png ├── drift.png ├── error_by_distance_and_year.png ├── 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