Merge pull request #278 from nextstrain/james/clade-i-tweaks

Clade-I tweaks
nextstrain · Nov 4, 2024 · 85364bc · 85364bc
2 parents cddd5f2 + fade79a
commit 85364bc
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Showing 7 changed files with 672 additions and 4 deletions.
diff --git a/phylogenetic/defaults/clade-i/auspice_config.json b/phylogenetic/defaults/clade-i/auspice_config.json
@@ -21,6 +21,16 @@
       "title": "Country",
       "type": "categorical"
     },
+    {
+      "key": "division",
+      "title": "Province",
+      "type": "categorical"
+    },
+    {
+      "key": "location",
+      "title": "Health Zone",
+      "type": "categorical"
+    },
     {
       "key": "host",
       "title": "Host",
@@ -53,13 +63,16 @@
     }
   ],
   "geo_resolutions": [
-    "country"
+    "region",
+    "country",
+    "division",
+    "location"
   ],
   "display_defaults": {
     "color_by": "country",
     "map_triplicate": true,
     "distance_measure": "num_date",
-    "transmission_lines": false
+    "transmission_lines": true
   },
   "filters": [
     "country",

diff --git a/phylogenetic/defaults/clade-i/config.yaml b/phylogenetic/defaults/clade-i/config.yaml
@@ -45,8 +45,9 @@ clock_rate: 1.465e-06
 clock_std_dev: 6.7e-07
 divergence_units: "mutations"
 
+
 traits:
-  columns: "country"
+  columns: region country
   sampling_bias_correction: 3
 
 ## recency
@@ -56,3 +57,6 @@ mask:
   from_beginning: 800
   from_end: 6422
   maskfile: "defaults/mask.bed"
+
+colors:
+  ignore_categories: "division location"