Merge pull request #99 from nextstrain/location-threshold

Reduce location count thresholds
nextstrain · May 9, 2024 · 00b9f23 · 00b9f23
2 parents fb9c7bb + 76f9149
commit 00b9f23
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -16,7 +16,7 @@ prepare_data:
     nextstrain_clades:
       global:
         included_days: 150
-        location_min_seq: 100
+        location_min_seq: 50
         location_min_seq_days: 30
         excluded_locations: "defaults/global_excluded_locations.txt"
         prune_seq_days: 12
@@ -25,7 +25,7 @@ prepare_data:
     pango_lineages:
       global:
         included_days: 150
-        location_min_seq: 300
+        location_min_seq: 150
         location_min_seq_days: 30
         excluded_locations: "defaults/global_excluded_locations.txt"
         prune_seq_days: 12
@@ -36,7 +36,7 @@ prepare_data:
     nextstrain_clades:
       global:
         included_days: 150
-        location_min_seq: 100
+        location_min_seq: 50
         location_min_seq_days: 30
         excluded_locations: "defaults/global_excluded_locations.txt"
         prune_seq_days: 12
@@ -45,7 +45,7 @@ prepare_data:
     pango_lineages:
       global:
         included_days: 150
-        location_min_seq: 300
+        location_min_seq: 150
         location_min_seq_days: 30
         excluded_locations: "defaults/global_excluded_locations.txt"
         prune_seq_days: 12

diff --git a/viz/src/App.jsx b/viz/src/App.jsx
@@ -31,7 +31,7 @@ function App() {
         <p>
           Each line represents the estimated frequency of a particular clade through time.
           Equivalent Pango lineage is given in parenthesis, eg clade 23A (lineage XBB.1.5). Only
-          locations with more than 100 sequences from samples collected in the previous 150 days are
+          locations with more than 50 sequences from samples collected in the previous 30 days are
           included. Results last updated {mlrCladesData?.modelData?.get('updated') || 'loading'}.
         </p>
         <div id="cladeFrequenciesPanel" class="panelDisplay"> {/* surrounding div(s) used for static-images.js script */}
@@ -54,7 +54,7 @@ function App() {
         <p>
           Each line represents the estimated frequency of a particular Pango lineage through time.
           Lineages with fewer than 350 observations are collapsed into parental lineage. Only
-          locations with more than 300 sequences from samples collected in the previous 150 days are
+          locations with more than 150 sequences from samples collected in the previous 30 days are
           included. Results last updated {mlrLineagesData?.modelData?.get('updated') || 'loading'}.
         </p>
         <div id="lineageFrequenciesPanel" class="panelDisplay">