Data
This directory contains working sets for h3, h1, vic and yam. These files were produced with the following pipeline:
- Clean sequences (remove outliers and pre-2000 sequences)
- Extract locations from strain names
- Combine locations into the 9 canonical regions
- Label dates as precise to the day, month or year
- Subsample sequences, preferring more precise dates or longer sequences
Sample counts and distributions
Full is all samples present post-2000. Small is selecting at most 14 (13 for USA) per year for H3, 30 (28 for USA) per year for H1, 30 (24 for USA) per year for Vic, 40 (25 for USA) per year for Yam. Large is selecting at most 50 (40 for USA) per year for H3, 80 (45 for USA) per year for H1, 80 (45 for USA) per year for Vic, 80 (40 for USA) per year for Yam. These sampling strategies resulting in similar overall counts across space and time.
| Lineage | Full | Small | Large |
|---|---|---|---|
| H3N2 | 8306 | 1391 | 4006 |
| H1N1 | 3318 | 1372 | 2144 |
| B/Vic | 2247 | 1394 | 1999 |
| B/Yam | 1556 | 1241 | 1455 |