corneliusroemer
commented
1 year ago I think the text is wrong, as the config shows:
location_min_seq: 100
location_min_seq_days: 30So in reality, to be included, a location needs 100 sequences within 30 days of today. Would be good to relax this I think. Recent data is not the most important criterion. Some countries just don't have recent data, that doesn't mean they shouldn't be included if they have slightly more delayed data. So I think location_min_seq_days should be increased to something like 60 days at least.
In addition, the website/html should pull the description from the config file and not hard code so that doc and code are automatically synced.
Current Behavior
The website currently states for clade frequencies:
We show the following countries:
This doesn't seem to be correct, or at least missing important context, as when I look for countries with more than 100 sequences with collection date <150 days ago on covSpectrum (https://cov-spectrum.org/explore/World/AllSamples/from%3D2023-07-02%26to%3D2023-11-22/variants/international-comparison?&) I get the following countries:
Expected behavior
Brazil | 2781 | 2023-26 | 2023-45 New Zealand | 2668 | 2023-26 | 2023-43 Israel | 2617 | 2023-26 | 2023-45 Greece | 2469 | 2023-27 | 2023-40 Russia | 1963 | 2023-26 | 2023-44 Austria | 1411 | 2023-27 | 2023-46 Peru | 1254 | 2023-26 | 2023-43 Luxembourg | 1213 | 2023-27 | 2023-43 Portugal | 1198 | 2023-27 | 2023-45 Mexico | 1074 | 2023-26 | 2023-42 Croatia | 858 | 2023-27 | 2023-43 Chile | 787 | 2023-27 | 2023-43 Thailand | 773 | 2023-26 | 2023-43 Slovenia | 752 | 2023-26 | 2023-42 Colombia | 653 | 2023-26 | 2023-43 Ukraine | 652 | 2023-27 | 2023-44 Taiwan | 581 | 2023-26 | 2023-45 South Africa | 493 | 2023-27 | 2023-41 Turkey | 465 | 2023-28 | 2023-40 Poland | 459 | 2023-28 | 2023-45 Norway | 441 | 2023-26 | 2023-44 Romania | 364 | 2023-27 | 2023-40 Argentina | 359 | 2023-26 | 2023-38 Malaysia | 359 | 2023-26 | 2023-43 Costa Rica | 341 | 2023-26 | 2023-43 Guatemala | 321 | 2023-27 | 2023-40 India | 285 | 2023-26 | 2023-44 Georgia | 272 | 2023-27 | 2023-40 Mauritius | 270 | 2023-27 | 2023-44 Bulgaria | 254 | 2023-27 | 2023-43 Dominican Republic | 200 | 2023-27 | 2023-35
Notably, we include Iceland with only 700 sequences but exclude Brazil with 2500