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Use population-based weighted sampling for global builds
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Extend the weighted sampling approach from regional builds to global
builds. This comes with the added benefit of simplifying logic to avoid
region/country-specific max_sequences.
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@victorlin
victorlin committed Sep 30, 2024
1 parent d6de734 commit ae764bb
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281 changes: 18 additions & 263 deletions nextstrain_profiles/nextstrain-gisaid-21L/builds.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -287,297 +287,52 @@ subsampling:
# Custom subsampling logic for global region over 1m
# 5125 total (expect ~3400)
# 4:1 ratio of recent to early
# all eight regions equal except Oceania at 20%
nextstrain_global_1m:
africa_early:
early:
group_by: "country year month"
max_sequences: 150
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=Africa'"
asia_early:
group_by: "country year month"
max_sequences: 200
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china_early:
group_by: "division year month"
max_sequences: 175
max_date: "--max-date 1M"
exclude: "--exclude-where 'country!=China'"
europe_early:
group_by: "country year month"
max_sequences: 125
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=Europe'"
india_early:
group_by: "division year month"
max_sequences: 175
max_date: "--max-date 1M"
exclude: "--exclude-where 'country!=India'"
north_america_early:
group_by: "division year month"
max_sequences: 100
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=North America'"
south_america_early:
group_by: "country year month"
max_sequences: 90
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=South America'"
oceania_early:
group_by: "division year month"
max_sequences: 15
group_by_weights: "defaults/population_weights.tsv"
max_sequences: 1025
max_date: "--max-date 1M"
exclude: "--exclude-where 'region!=Oceania'"
africa_recent:
group_by: "country week"
max_sequences: 600
min_date: "--min-date 1M"
exclude: "--exclude-where 'region!=Africa'"
asia_recent:
group_by: "country week"
max_sequences: 800
min_date: "--min-date 1M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china_recent:
group_by: "division week"
max_sequences: 700
min_date: "--min-date 1M"
exclude: "--exclude-where 'country!=China'"
europe_recent:
recent:
group_by: "country week"
max_sequences: 500
min_date: "--min-date 1M"
exclude: "--exclude-where 'region!=Europe'"
india_recent:
group_by: "division week"
max_sequences: 700
max_sequences: 4100
min_date: "--min-date 1M"
exclude: "--exclude-where 'country!=India'"
north_america_recent:
group_by: "division week"
max_sequences: 400
min_date: "--min-date 1M"
exclude: "--exclude-where 'region!=North America'"
south_america_recent:
group_by: "country week"
max_sequences: 360
min_date: "--min-date 1M"
exclude: "--exclude-where 'region!=South America'"
oceania_recent:
group_by: "division week"
max_sequences: 60
min_date: "--min-date 1M"
exclude: "--exclude-where 'region!=Oceania'"

# Custom subsampling logic for global region over 2m
# 5125 total (expect ~3400)
# 4:1 ratio of recent to early
# all eight regions equal except Oceania at 20%
nextstrain_global_2m:
africa_early:
group_by: "country year month"
max_sequences: 150
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=Africa'"
asia_early:
group_by: "country year month"
max_sequences: 200
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china_early:
group_by: "division year month"
max_sequences: 175
max_date: "--max-date 2M"
exclude: "--exclude-where 'country!=China'"
europe_early:
early:
group_by: "country year month"
max_sequences: 125
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=Europe'"
india_early:
group_by: "division year month"
max_sequences: 175
max_date: "--max-date 2M"
exclude: "--exclude-where 'country!=India'"
north_america_early:
group_by: "division year month"
max_sequences: 100
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=North America'"
south_america_early:
group_by: "country year month"
max_sequences: 90
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=South America'"
oceania_early:
group_by: "division year month"
max_sequences: 15
group_by_weights: "defaults/population_weights.tsv"
max_sequences: 1025
max_date: "--max-date 2M"
exclude: "--exclude-where 'region!=Oceania'"
africa_recent:
recent:
group_by: "country week"
max_sequences: 600
max_sequences: 4100
min_date: "--min-date 2M"
exclude: "--exclude-where 'region!=Africa'"
asia_recent:
group_by: "country week"
max_sequences: 800
min_date: "--min-date 2M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china_recent:
group_by: "division week"
max_sequences: 700
min_date: "--min-date 2M"
exclude: "--exclude-where 'country!=China'"
europe_recent:
group_by: "country week"
max_sequences: 500
min_date: "--min-date 2M"
exclude: "--exclude-where 'region!=Europe'"
india_recent:
group_by: "division week"
max_sequences: 700
min_date: "--min-date 2M"
exclude: "--exclude-where 'country!=India'"
north_america_recent:
group_by: "division week"
max_sequences: 400
min_date: "--min-date 2M"
exclude: "--exclude-where 'region!=North America'"
south_america_recent:
group_by: "country week"
max_sequences: 360
min_date: "--min-date 2M"
exclude: "--exclude-where 'region!=South America'"
oceania_recent:
group_by: "division week"
max_sequences: 60
min_date: "--min-date 2M"
exclude: "--exclude-where 'region!=Oceania'"

# Custom subsampling logic for global region over 6m
# 5125 total (expect ~3400)
# 4:1 ratio of recent to early
# all eight regions equal except Oceania at 20%
nextstrain_global_6m:
africa_early:
group_by: "country year month"
max_sequences: 150
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=Africa'"
asia_early:
group_by: "country year month"
max_sequences: 200
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china_early:
group_by: "division year month"
max_sequences: 175
max_date: "--max-date 6M"
exclude: "--exclude-where 'country!=China'"
europe_early:
group_by: "country year month"
max_sequences: 125
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=Europe'"
india_early:
group_by: "division year month"
max_sequences: 175
max_date: "--max-date 6M"
exclude: "--exclude-where 'country!=India'"
north_america_early:
group_by: "division year month"
max_sequences: 100
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=North America'"
south_america_early:
early:
group_by: "country year month"
max_sequences: 90
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=South America'"
oceania_early:
group_by: "division year month"
max_sequences: 15
group_by_weights: "defaults/population_weights.tsv"
max_sequences: 1025
max_date: "--max-date 6M"
exclude: "--exclude-where 'region!=Oceania'"
africa_recent:
group_by: "country year month"
max_sequences: 600
min_date: "--min-date 6M"
exclude: "--exclude-where 'region!=Africa'"
asia_recent:
group_by: "country year month"
max_sequences: 800
min_date: "--min-date 6M"
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china_recent:
group_by: "division year month"
max_sequences: 700
min_date: "--min-date 6M"
exclude: "--exclude-where 'country!=China'"
europe_recent:
group_by: "country year month"
max_sequences: 500
min_date: "--min-date 6M"
exclude: "--exclude-where 'region!=Europe'"
india_recent:
group_by: "division year month"
max_sequences: 700
min_date: "--min-date 6M"
exclude: "--exclude-where 'country!=India'"
north_america_recent:
group_by: "division year month"
max_sequences: 400
min_date: "--min-date 6M"
exclude: "--exclude-where 'region!=North America'"
south_america_recent:
recent:
group_by: "country year month"
max_sequences: 360
max_sequences: 4100
min_date: "--min-date 6M"
exclude: "--exclude-where 'region!=South America'"
oceania_recent:
group_by: "division year month"
max_sequences: 60
min_date: "--min-date 6M"
exclude: "--exclude-where 'region!=Oceania'"

# Custom subsampling logic for global region over all-time
# 4320 total (expect ~3200)
# all eight regions equal except Oceania at 20%
nextstrain_global_all_time:
africa:
group_by: "country year month"
max_sequences: 750
exclude: "--exclude-where 'region!=Africa'"
asia:
all:
group_by: "country year month"
max_sequences: 1000
exclude: "--exclude-where 'region!=Asia' 'country=China' 'country=India'"
china:
group_by: "division year month"
max_sequences: 875
exclude: "--exclude-where 'country!=China'"
europe:
group_by: "country year month"
max_sequences: 625
exclude: "--exclude-where 'region!=Europe'"
india:
group_by: "division year month"
max_sequences: 875
exclude: "--exclude-where 'country!=India'"
north_america:
group_by: "division year month"
max_sequences: 500
exclude: "--exclude-where 'region!=North America'"
south_america:
group_by: "country year month"
max_sequences: 450
exclude: "--exclude-where 'region!=South America'"
oceania:
group_by: "division year month"
max_sequences: 75
exclude: "--exclude-where 'region!=Oceania'"
group_by_weights: "defaults/population_weights.tsv"
max_sequences: 4320

# Root to clade 21L
refine:
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