Merge pull request #1130 from nextstrain/build-specific-narrow-bandwidth

Allow build-specific --narrow-bandwidth param in frequencies

defaults/parameters.yaml

@@ -137,18 +137,29 @@ ancestral:
 # Frequencies settings
 frequencies:
 
-  # min_date is set by default to 1 year before present
-  # but can be explicitly set if desired
+  # default settings that can be over-ridden for specific builds
+  default:
+
+    # min_date is set by default to 1 year before present
+    min_date: "1Y"
+
+    # max_date is set by default to present date - recent_days_to_censor
+
+    # KDE bandwidths in proportion of a year to use per strain.
+    # using 1M bandwidth by default
+    narrow_bandwidth: 0.0833
+
+
+  # settings that can be over-ridden across all builds, but not for specific builds
+  recent_days_to_censor: 0
 
   # Number of weeks between pivots
   pivot_interval: 1
 
   # Measure pivots in weeks
   pivot_interval_units: "weeks"
 
-  # KDE bandwidths in proportion of a year to use per strain.
-  # using 15 day bandwidth
-  narrow_bandwidth: 0.041
+  # Weight of KDE that uses wide bandwidth
   proportion_wide: 0.0
 
   # Diffusion frequency settings

docs/src/reference/workflow-config-file.rst

@@ -983,13 +983,30 @@ columns
 
 frequencies
 -----------
-- Valid attributes:
+-  type: object
+-  description: Parameters for specifying tip frequency calculations via ``augur frequencies``
+-  examples:
+
+.. code:: yaml
+
+   frequencies:
+     pivot_interval_units: "weeks"
+     default:
+       min_date: "6M"
+       narrow_bandwidth: 0.038
+     global_1m:
+       min_date: "1M"
+       narrow_bandwidth: 0.019
+     global_2020_to_2022:
+       min_date: "2020-01-01"
+       max_date: "2022-01-01"
+       narrow_bandwidth: 0.076
+
+Each named traits configuration (``default`` or build-named) supports specification of ``min_date``, ``max_date`` and ``narrow_bandwidth``. Other parameters can only be specified across all builds.
 
 .. contents::
    :local:
 
-.. _min_date-1:
-
 min_date
 ~~~~~~~~
 

nextstrain_profiles/nextstrain-gisaid-21L/builds.yaml

@@ -431,115 +431,62 @@ traits:
 # narrow_bandwidth = 0.019 or 7 days for "1m" and "2m"
 # narrow_bandwidth = 0.038 or 14 days for "6m" and "all-time"
 frequencies:
+  default:
+    min_date: "2020-01-01"
+    narrow_bandwidth: 0.038
   global_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   global_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   global_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  global_all-time:
-    min_date: "2022-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   africa_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   africa_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   africa_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  africa_all-time:
-    min_date: "2022-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   asia_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   asia_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   asia_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  asia_all-time:
-    min_date: "2022-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   europe_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   europe_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   europe_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  europe_all-time:
-    min_date: "2022-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   north-america_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   north-america_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   north-america_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  north-america_all-time:
-    min_date: "2022-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   oceania_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   oceania_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   oceania_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  oceania_all-time:
-    min_date: "2022-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   south-america_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   south-america_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   south-america_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  south-america_all-time:
-    min_date: "2022-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7

nextstrain_profiles/nextstrain-gisaid/builds.yaml

@@ -422,119 +422,62 @@ traits:
 # narrow_bandwidth = 0.019 or 7 days for "1m" and "2m"
 # narrow_bandwidth = 0.038 or 14 days for "6m" and "all-time"
 frequencies:
-  reference:
+  default:
     min_date: "2020-01-01"
     narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   global_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   global_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   global_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  global_all-time:
-    min_date: "2020-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   africa_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   africa_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   africa_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  africa_all-time:
-    min_date: "2020-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   asia_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   asia_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   asia_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  asia_all-time:
-    min_date: "2020-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   europe_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   europe_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   europe_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  europe_all-time:
-    min_date: "2020-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   north-america_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   north-america_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   north-america_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  north-america_all-time:
-    min_date: "2020-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   oceania_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   oceania_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   oceania_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  oceania_all-time:
-    min_date: "2020-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
   south-america_1m:
     min_date: "1M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   south-america_2m:
     min_date: "2M"
     narrow_bandwidth: 0.019
-    recent_days_to_censor: 7
   south-america_6m:
     min_date: "6M"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7
-  south-america_all-time:
-    min_date: "2020-01-01"
-    narrow_bandwidth: 0.038
-    recent_days_to_censor: 7